An eighth-minute own goal from Aberdeen's Stevie Smith and midfielder Jamie Adams' second-half header proved the difference between the sides as the Dons failed to force Saints keeper Peter Enckelman into action.
The only bright spot for Aberdeen was the return of teenager Fraser Fyvie after a cruciate ligament injury, the midfielder coming off the bench midway through the second half.
Fellow youngster Peter Pawlett dropped from the bench despite his winning goal against Inverness Caledonian Thistle last Saturday, having picked up a hamstring injury. Striker Michael Paton also missed out with a calf injury.
Josh Magennis returned to the starting lineup for the Dons against a Saints side who welcomed Steven Anderson and Michael Duberry back from suspension.
Alan Maybury and Danny Grainger made way, while Liam Craig also returned in place of Danny Invincibile.
As early as the first minute, the Saints had the home goal under threat as Andy Jackson cut in from the left before pulling a right-foot shot wide of the near post.
They took a deserved lead after just eight minutes as Smith turned a Jackson cross beyond his own goalkeeper under pressure from Peter MacDonald.
And they perhaps should have had a penalty when MacDonald seemed to be bundled to the ground by Zander Diamond while chasing a Jackson pass four minutes later, but referee John MacKendrick was unmoved.
The visitors threatened again after 26 minutes as Murray Davidson won the ball in the Dons box, but there were no takers for his inviting cross.
Aberdeen captain Derek Young became the first man to enter MacKendrick's book, penalised for dissent after the Perth side were awarded a rather soft free kick.
Dons keeper Jamie Langfield kept his side in touch with a fine save just beyond the half-hour, turning Chris Millar's volley past the post.
It was just 10 minutes from the interval when Sone Aluko blazed over with the Dons' first clear sight of goal, and Maguire did similar with an ambitious effort shortly after.
A poor first half for the Dons got worse as Diamond was forced off through injury five minutes before the break.
A foul which left Jackson in need of treatment saw Rob Milsom pick up a booking after 52 minutes, but the Saints striker was back on his feet and through on goal a minute later, only for his shot to be blocked by the face of Langfield.
Saints first change saw Maybury replace Scotland Under-21 star Murray Davidson, allowing Craig to step forward into a midfield role and within a minute the visitors doubled their lead.
It was Craig who swung in a corner from the right, and Jamie Adams found space to bullet a header beyond the helpless Langfield.
The loudest cheer of the afternoon was reserved for Fyvie, who made his entrance after 66 minutes, replacing the ineffective Nick Blackman.
Aberdeen used their final change to introduce U19 captain Nicky Low, and the youngster injected a bit of life to their performance, one strong, direct run with eight minutes left ending with his cross striking the bar.
Craig sent a late snap-shot past the upright, while boss Derek McInnes gave late cameo appearances to young strikers Stephen Reynolds and Stevie May.