The First Minister said she and others within the Scottish Government felt “let down” by Mr Salmond’s conduct and that she would not apologise for his behaviour.
She claimed one of the differences between her and her predecessor was she had never claimed to be “infallible”.
Ms Sturgeon’s comments came as she apologised to the public for the Scottish Government’s handling of the judicial review and to the two complainers in the case for the failures of the complaints process, which led to £500,000 of taxpayers’ money being lost.
In a marathon session of more than eight hours in Holyrood, the First Minister rejected accusations that she breached the ministerial code and defended her government’s actions in relation to the development of the harassment complaints procedure.
However, outstanding questions on the nature of meetings between her and Mr Salmond’s former chief of staff Geoff Aberdein remain unanswered, as do allegations a senior official within Ms Sturgeon’s office passed the name of a complainer to Mr Aberdein in a meeting in early March.
The First Minister explicitly rejected the “characterisation” of those meetings by opposition MSPs and said that “to the best of my knowledge” such events did not take place.
Ms Sturgeon also rejected several of the claims central to Mr Salmond’s evidence, including that the timing of the judicial review was “gamed” so the criminal case could take over, and the complaints procedure had been established to “get” the former first minister.
A vote of no confidence in both Ms Sturgeon and her deputy John Swinney remain on the table after being submitted by the Scottish Conservatives, with Scottish Labour’s member on the inquiry Jackie Baillie saying serious questions around the First Minister’s conduct still need to be answered.
At the start of her long-awaited oral evidence session, Ms Sturgeon said she would never forget the day Mr Salmond arrived at her house to tell her of the investigation her government was conducting into allegations against him.
Apologising to Scottish taxpayers and the two women who raised the complaints against Mr Salmond, Ms Sturgeon said she deeply regretted how the case had been handled.
In an emotional opening statement, she said: “A number of women made complaints against Alex Salmond s behaviour. The government, despite the mistake it undoubtedly made, tried to do the right thing.”
“As First Minister I tried to avoid the age old pattern of allowing a powerful man of using his status and connections to get what he wants.”
She added that when Mr Salmond informed her of the complaints, she viewed it as constituting “deeply inappropriate behaviour”.
Ms Sturgeon later denied she had any knowledge of the leak of a complainant’s name to Mr Aberdein or of the leak of the government’s investigation into Mr Salmond to the Daily Record.
Pressed on claims, corroborated by other witnesses, that a senior member of her team had leaked the name of one of the women involved to Mr Aberdein, Ms Sturgeon was challenged on the “extraordinary breach of confidentiality” that constituted a “sackable offence” by Ms Baillie.
Ms Sturgeon said she refused to accept Ms Baillie’s “characterisation” of what had happened.
"I am not accepting that that happened, therefore I am clearly not accepting that was authorised,” she said, saying the event was a "matter of contention".
Ms Sturgeon added that she believed Mr Salmond had deduced the name of one complainant through the use of the Scottish Government’s Flickr account, while he had prior knowledge of the identity of the other complainant.
A statement from Mr Salmond released during Ms Sturgeon’s testimony said he had submitted an official complaint to the permanent secretary on the alleged conduct of the official relating to the disclosure of the name of a complainant
Mr Salmond’s legal team has also handed over more evidence, including a witness statement and the minutes of the Commission and Diligence to the committee.
Ms Sturgeon also dismissed claims of a “plot” to undermine the former first minister – an allegation she claimed was “not based in any semblance of fact or semblance of evidence”.
Rejecting allegations that failing to intervene in the process and failing to record her meeting with Mr Salmond on April 2, 2018 with the civil service breached the ministerial code, the First Minister said concerns about the potential impact on the impartiality, independence and confidentiality of the process drove her decisions.
She said: “The thing that I was absolutely adamant about that I would not on his behalf, despite all I’ve just said about loyalty and friendship, I would not try to influence this process in the way he wanted me to because I think that would have been inappropriate.
"That is the touchstone on this that I believe I was right to do. I know I have heard this afternoon different views on that, but I believe that was the right decision to make.”
During a line of questioning from Scottish Conservative MSP Murdo Fraser, Ms Sturgeon was asked whether she would apologise for asking the Scottish people to trust Mr Salmond.
In an emotional response, she refused.
The First Minister said: “I have learned things about Alex Salmond over the last couple of years that have made me rethink certain things I thought about him.
"As I was watching him on Friday lashing out, that’s my words, against us, I don’t know whether he ever reflects on the fact that many of us, including me, feel very let down by him.”
She added: "I trusted him and I am not going to apologise for the behaviour of somebody else.
"If I have things in my behaviour to apologise for, I will apologise, but I do not think it is reasonable to ask me to apologise for the behaviour, some of which he will deny of course, of Alex Salmond.
"I think the only person who should apologise for any behaviour on his part, which he was asked to do on Friday and failed to do, is Alex Salmond.”
In her closing remarks, Ms Sturgeon also launched a staunch defence of Scotland’s institutions and those who lead them.
She said: “I would put it to people this is seen as an example of the institutions of the country – the independent institutions of the country – doing their job.
"Out of this comes the message that no matter how powerful you are or were, no matter your status or connections, if you are accused of serious offences they will be investigated and you will have the chance to defend yourself in court.
"That is how these things should work.
"Mistakes have been made by government and that is undeniable, but the idea that because somebody doesn’t like what happened over the past couple of years we allow this attack to be made on the very fundamentals of our democracy, I just find deeply distressing, deeply unfair, and actually whatever you think of me, the SNP, the Scottish Government, deeply injurious to the health and wellbeing of our democracy.”
Responding to the session after it finished, Ms Baillie said “serious questions” about the First Minister’s conduct remained unanswered.
She said: “The First Minister’s appearance was welcome, but quite frankly we are not much further forward in understanding her role in this catastrophic failure of the Scottish Government.
“Most galling of all was the First Minister’s complete failure to understand the obstruction that this committee has faced and continues to face. The First Minister promised the committee that it would receive all the information that it needed – this now sounds like a bad joke.
“On several occasions, Nicola Sturgeon has stated that she did not offer to intervene in the process in favour of Mr Salmond. This has been disputed by the testimony provided by several witnesses. It is simply unbelievable that the reason for this discrepancy in accounts is that she was trying to let Mr Salmond down gently.”
Reacting to the session, Scottish Conservative leader Douglas Ross repeated calls for Ms Sturgeon to resign, claiming her evidence was a “litany of lies and abject failures”.
The Moray MP said: “The abiding memory of this evidence session will be Nicola Sturgeon proclaiming ‘I can’t recall’ on repeat. She dodged and evaded almost every difficult question.
“The First Minister vividly remembers the details she believes exonerate her, then forgets entirely anything that damages her.
“It’s not remotely credible, in fact it’s plainly absurd, for the First Minister to ask us to believe her account of a secret meeting that she claims to have forgotten entirely, instead of the evidence of multiple credible witnesses.
“The litany of lies and abject failures is too much for any First Minister to survive. The evidence is overwhelming. She must go.”
Commenting following the conclusion of the session, a spokesperson for the First Minister said the session had showed the opposition had “completely failed to substantiate” the allegations and “absurd conspiracy theories” against her.
The spokesperson said: “The First Minister today dismantled all of the claims which have been made against her.
“The First Minister gave a clear, open and transparent account to the committee and directly addressed all of the issues raised. She was happy to take all of their questions and gave evidence for as long as the committee members wanted.
“She now looks forward to receiving the conclusions of the committee’s report, and to report of James Hamilton, the independent adviser on the ministerial code.”