Connor Ronan netted twice and Marcus Fraser was also on the scoresheet to leave the Dons winless in eight games.
Stephen Glass' men were 2-1 ahead through goals from Scott Brown and Christian Ramirez when Teddy Jenks was sent off early in the second half for a second booking.
St Mirren made one change from the team that had drawn against Hibernian, with Ethan Erhahon coming in for Dylan Reid.
Aberdeen made three changes. Ryan Hedges returned from a six-week injury lay-off to start, with Jenks and Jonny Hayes also included, meaning Funso Ojo, Jay Emmanuel-Thomas and Austin Samuels were left out.
Jenks was involved in the first attack of the game, crossing into a dangerous area for Hayes whose shot was saved by Jak Alnwick.
It was the home side that went in front, though, after 14 minutes. Erhahon picked out Ronan and his shot beat Joe Lewis with the aid of a deflection off David Bates.
The Dons were level just four minutes later. Calvin Ramsay's free-kick was headed down by Ramirez and bounced off Brown and trickled in.
Jenks then had a shot saved before Aberdeen moved in front after 34 minutes as another Ramsay free-kick was bulleted in by the unmarked Ramirez.
St Mirren tried to rally but an Alan Power effort from a corner was well over the bar before a low free-kick from Scott Tanser early in the second half was well saved by Lewis.
Aberdeen responded with a Lewis Ferguson effort that went high into the stand before they were reduced to 10 men when Jenks was shown a second yellow card for a foul on Jamie McGrath having previously been booked in the first half.
St Mirren took advantage of the extra man just seven minutes later. McGrath played in Ronan who took his time before finishing low past Lewis.
And it got even better for the home side when they went back in front after 61 minutes. Fraser floated in a ball for Curtis Main who challenged with Lewis but didn't seem to get a touch as it sailed in.
St Mirren should have had a fourth but Eamonn Brophy somehow missed at the back post after a great ball from Tanser.
Aberdeen almost capitalised moments later but Ferguson's volley was similarly off target before Main headed over from Ronan's cross.