The match appeared to be heading for stalemate when referee Calum Murray pointed to the spot after Eric Djemba-Djemba slid in on Peter Pawlett and upended the Dons forward on the 18-yard line as he tried to burst into the box.
In the absence of injured midfielder Barry Robson, new Aberdeen striker Rooney stepped up and confidently sent goalkeeper Marian Kello the wrong way with his low penalty 10 minutes from time.
In a first half of limited chances, Paul McGowan swivelled inside the Aberdeen box and hooked a shot just wide of Jamie Langfield's left post.
At the other end of the pitch Niall McGinn crashed a free-kick into the St Mirren defensive wall from 25 yards.
Steven Thompson came close to opening the scoring three minutes after the break when he beat Russell Anderson to a Kenny McLean cross only to send his half-volley narrowly wide.
Aberdeen responded as McGinn and Nicky Low worked a short-corner and the latter's delivery found Andrew Considine whose header forced Kello into a diving save.
And Considine caused further problems for the Buddies as he rose to flick on a long throw-in which just evaded McGinn as he arrived at the back post.
Former Dons winger Gregg Wylde almost rescued a point for St Mirren two minutes from the end but his powerful volley from eight yards was kept out by a superb reflex save from Langfield.
Aberdeen then squandered the opportunity to add a second when Rooney's fierce shot was parried back to him by Kello, and the Irishman over-hit his square pass to McGinn who was lurking in front of an empty goal.