Connor Ronan's curled effort made the difference as St. Mirren picked up all three Premiership points.
Aberdeen have now failed to win away to St Mirren in the league since December 2018.
“It was a disappointing performance,” said manager Stephen Glass. “One moment of quality in the game wins it for St Mirren. I think it’s disappointing given the amount of possession we had that one of our players didn’t do it.
“We gave up quite a cheap goal, a brilliant finish from their player but a cheap goal from our point of view.
“We didn’t do enough to threaten their goal. As a result, you get what you get.”