Rooney took his goal tally for the season to 23 with two predatory first-half strikes and Mark Reynolds’ header capped a fine afternoon for the men in red.
Derek McInnes’ rejuvenated side are now unbeaten in their last 13 league matches, and they will be eager to make it 14 next weekend – when they travel to Celtic Park for what promises to be a Sky Live classic.
Dons midfielder Ryan Jack produced an early cross but Rooney’s finish could not match the quality of the delivery.
The play continued to flow towards Marc Ridgers’ goal and Rooney was centre stage again as he produced a cute flick from Shay Logan’s assist but the ball drifted wide.
Rooney was claiming a goal after the ball was scrambled off the line – but any disquiet was soon forgotten as Andy Considine headed Kenny McLean’s delivery back across goal and Rooney (21) made no mistake this time from two yards out.
St Mirren, whose five wins this season have all come away from home, battled for a toehold with recent arrivals James Dayton and Yohan Arquin to the fore but the home side were quick to break and Peter Pawlett saw his shot go wide after a promising surge.
It was Aberdeen who continued to look the more potent side and the fans were still taking their seats after the half-time pie-break when Niall McGinn found McLean to set up Rooney (48) – and the striker tucked in his second of the afternoon.
Reynolds (70) was the next to get in on the act as he headed in the excellent McGinn’s corner for his third goal of the season.
Jim Goodwin and John McGinn had token late efforts for St Mirren but there was to be no consolation for Gary Teale’s strugglers, who now sit joint-bottom after Ross County’s win at Partick Thistle.