In August, Scott initiated the investigation into a "disappointing" Olympic campaign that produced three medals from a target of five to seven.
A key finding of the report required Australia-based Scott to relocate to Britain, something he was unable to do.
Scott, who has been performance director since 2007, will step aside at the end of the month.
The Australian's removal allows British swimming to begin the search for a new performance director as attention turns to the next Olympics in Rio in four years' time.
"I respect this conclusion from the performance review I initiated following our results in London," Scott said.
"I wanted to make sure we left no stone unturned in understanding why we didn't achieve our goals.
"One of the key findings of the review requires a change to my current working practice by being based in Britain. However, for personal and family reasons, I'm unable to meet this recommendation and therefore offered my resignation."
British Swimming's performance director Michael Scott has resigned following a review into results at London 2012.