In a long-awaited oral evidence session to the Holyrood committee investigating the government’s handling of the original inquiry, 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.
And in an emotional statement, she said she had “searched” Mr Salmond’s statement to the committee last week for “any sign of regret or reflection” on his part and had found none.
Ms Sturgeon said it had been right for the government to put in place a new procedure to deal with any historic complaints of sexual harassment in the wake of the #MeToo movement.
But she added: "As a result of a very serious mistake made in the investigation of the complaint, two women were failed and taxpayers’ money was lost, I deeply regret that.
“Although I wasn't aware of the error at the time, I am the head of the Scottish Government, so I want to say sorry to the two women involved and the Scottish public.”
Ms Sturgeon also said Mr Salmond’s claims of a "malicious plan” was “not based in any fact”.
“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,” she said.
“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.
“The police conducted an independent criminal investigation, the Crown Office, as it does in prosecutions every single week, considered the evidence and found there was a case to answer. A court and jury did their jobs and now this committee and an independent investigation are considering what happened and why.”
She also contradicted the claims of Mr Salmond, and those of his former counsel Duncan Hamilton QC, about the meeting at her house on April 2, 2018, that Ms Sturgeon knew what the meeting was about.
"When he arrived at my house he was insistent he speak to me entirely privately, away from his former chief of staff Geoff Aberdein, Duncan Hamilton, and my chief of staff who was with me,” she said.
"That would have seemed unnecessary had there already been a shared understanding on the part of all of us.
"He then showed me a letter from the Permanent Secretary [Leslie Evans]. This set out the fact complaints had been made against him by two individuals … and set out what he was alleged to have done.
“Reading this letter is a moment in my life I will never forget.
"And although he denied the allegations, he gave me his account of one of the incidents, which he said he had apologised for at the time. What he described, constituted in my view, deeply inappropriate behaviour on his part, perhaps another reason that moment is so deeply embedded in my mind.”
Ms Sturgeon went further and said the investigation into potential breaches of the ministerial code, being conducted by James Hamilton QC, meant “he is able to see and hear material that this committee cannot, including as I understand it from people who were party to discussions that others who were not party to those discussions, are seeking to attest to”.
And she dismissed the importance of a “conversation” she had with Mr Aberdein on March 29, which has been claimed to be pivotal by Mr Salmond, and which she had previously said she forgot. She said her recollection of it “was different” to Mr Aberdein’s and she did not attach the same “significance” to it as him.
She also claimed she believed Mr Salmond was considering resigning from the SNP – something he has denied.
"The purpose of it seemed to be to persuade me to meet with Alex as soon as possible, which I did agree to do,” she said.
"Geoff did indicate a harassment type issue had arisen, but my recollection is he did so in general terms.
"Since an approach from Sky News in November 2017 … I had harboured a lingering suspicion that such issues in relation to Mr Salmond might rear their head. So hearing of a potential issue would not in itself have been a massive shock.
"What I recall more strongly about the conversation was how worried Geoff seemed to be about Alex's welfare and state of mind, which as a friend concerned me. He also said he thought Alex might be considering resigning his party membership.
"It was these factors which led me to agree to meet him and it was these factors that placed the meeting on April 2 firmly in the personal and party space."
Ms Sturgeon told the committee she wished her memory of the meeting on March 29, 2018 was "more vivid".
But Ms Sturgeon said: "It was the detail of the complaints under the procedure that I was given on April 2 that was significant and indeed shocking. That was the moment at which any suspicions I had or general awareness there was a problem became actual and detailed knowledge."
She later said she was “relieved” to be in front of the committee, “but given all that has brought us to this moment, being here also makes me feel really sad”.
Ms Sturgeon added: “In all the legitimate consideration of this, sometimes the personal, human elements of this situation are lost. Alex spoke on Friday about what a nightmare the last couple of years have been for him and I don’t doubt that.
“I have thought often about the impact on him – he was someone I cared about for a long time. Which is why on Friday I was searching for any sign at all he recognised how difficult this has been for others too.
"First for women who believed his behaviour to them was inappropriate, but also for those of us who campaigned with him, worked for him and considered him a friend and now stand unfairly accused of plotting against him.
“He was acquitted by a jury of criminal conduct and that is beyond question, but I know, just from what he told me, that his behaviour was not always appropriate.
“Yet across six hours of testimony there was not a single word of regret, reflection or any acknowledgement of that I can only hope that in private the reality might be different.”
She went on: “I have never claimed to be infallible and searched my soul on this many times over. It may well be I didn’t get everything right, that’s for others to judge, but in one of the most invidious political and personal situations I have ever faced I believe I have acted appropriately and overall made the best judgements I could.
“For anyone willing to listen with an open mind I will seek to demonstrate that today.”