Judges ruled the UK Government’s policy on discharging untested patients into care homes south of the border was unlawful.
Ms Sturgeon said the guidance issued in Scotland was “broadly similar” to that in place in England, but not “identical”.
Speaking during First Minister's Questions, Scottish Labour leader Anas Sarwar asked: "Does the First Minister accept that her decision to send untested and positive patients into care homes in Scotland was unlawful, unreasonable, irrational and cost lives?"
Ms Sturgeon replied: “No, I don’t accept that, although these are matters now, rightly and properly, that will be scrutinised by the public inquiry that is under way in Scotland and, of course, the parallel public inquiry that will take place into these matters UK-wide.”
She said ministers "sought to take the best decisions based on the best scientific and clinical evidence that we had at any given time".
Mr Sarwar called the First Minister's answer “extraordinary and unthinkable", and listed guidance and advice from experts in the run-up to the introduction of a nationwide lockdown at the end of March 2020.
He said the-then health secretary, “as late as April 17”, was continuing to say there was “still not a strong case to test patients before discharge”.
Mr Sarwar said: “By the time Government changed guidance on April 21, nearly 3,000 untested people and 75 known positive cases had already been transferred into Scotland’s care homes.
“Does the First Minister accept, in the words of the families affected and impacted, that this was a shameful, unforgiveable, criminal act that cost lives in Scotland?”
Ms Sturgeon reiterated the guidance on care homes in Scotland was “broadly similar” to that in England and Wales, but "there were some differences".
She highlighted that asymptomatic transmission was being acknowledged despite “mixed views” about the risk.
The First Minister said Public Health Scotland also found there was “no clear statistical evidence” that hospital discharges were associated with outbreaks in care homes north of the border.
Mr Sarwar accused her of “ducking and diving”.
Ms Sturgeon told MSPs the human consequences of the pandemic are “embedded in my soul”, adding: “That does not mean my decisions and my actions and those of my Government should in any way not be subject to scrutiny.”
Earlier, Deputy First Minister John Swinney told Holyrood’s Covid-19 recovery committee the Scottish Government will “consider carefully” the High Court ruling.
Mr Swinney said Lady Poole’s Scottish Covid inquiry would examine the topic, and expressed “deep regret and sympathy” to everyone who had lost a loved one in a care home.
He said the judgment reflected circumstances in England and was “not directly comparable to the situation in Scotland”, but added: “We will, of course, consider carefully the issues that are raised by the judgment and beyond what I’ve said already, that will be the subject of further consideration.”
The remit of Lady Poole’s inquiry has an “explicit provision” to examine care homes, he said.