Following the resignation of John Coughlin, the 41-year-old was quickly promoted to the role of manager.
In his second full season in charge, MacPherson won the First Division title and secured promotion to the SPL.
The Buddies have since finished 11th, 10th, 11th and 10th in their four seasons in the 12-team top flight.
This season, St Mirren reached the final of the Co-operative Insurance Cup but lost out to a late goal from Rangers, despite their opponents having two players sent off.
Saints defender Jack Ross told BBC Scotland: "After the last game of the season, I don't think anybody expected anybody other than Gus to be in charge of the club when we reported back.
"When you are a footballer you see managers leave your club, sometimes because they have been so successful or sometimes because as a team you have failed, or perhaps been relegated.
"If that had happened, it might have been a decision we would have expected.
"But I'm surprised, given the timing of it, coming so quickly after the end of the season, maintaining our SPL status again, reaching the cup final; that, combined with the previous six seasons Gus had been in charge, make his tenure a success."
Chairman Stuart Gilmour declined to add to the statement released on the club's website.
Last week, Gilmour warned that the size of the first-team squad might be reduced amid cost-cutting measures for next season.
MacPherson has been the longest serving manager at St Mirren since WWII and leaves the club on the same day as director Gordon Scott, who has resigned from the board.
Scott had twice failed with bids to buy the shares of the consortium who hold a majority stake in the club.
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