The Dons were reduced to 10 men just after the restart when Rory McArdle was shown a straight red for a reckless lunge on winger Cleveland Taylor.
And the visitors left Pittodrie with all three points on Saturday when the unfortunate Zander Diamond headed Peter MacDonald's cross into his own net with less than 10 minutes remaining.
The result means the Dons have now taken only four points from the last possible 36 in the Scottish Premier League.
Aberdeen's only change from the side that lost 2-0 to Rangers saw defender Andrew Considine,
back available after a knee injury, replace Togolese midfielder Yoann Folly.
There was a place on the bench for Lithuanian striker Andrius Velicka who had missed the Ibrox match under the terms of his loan agreement.
St Johnstone came to Pittodrie on the back of four league defeats, having failed to score in each of the matches and conceding 12 in the process.
The Perth side also made only one change from the side that lost 2-0 to Hearts with Liam Craig, missing due to a calf injury, replaced by MacDonald.
The visitors had the first attempt at goal after five minutes when Jamie Adams, recently recalled from a loan spell at Dundee, dispossessed Dons skipper Paul Hartley and flashed a speculative shot from 25 yards harmlessly past the post.
A mix-up in the St Johnstone defence between Adams and Murray Davidson gifted Scott Vernon a chance at the other end but the striker's shot was well blocked by goalkeeper Peter Enckelman.
The visitors should have taken the lead after 22 minutes when MacDonald found Taylor unmarked at the back post but, with the goal at his mercy, the former Brentford winger's first-time effort bounced back off the post and away to safety.
The Dons created a chance at the other end when Hartley linked up with Clark Robertson but his curling effort sailed over the bar.
Sone Aluko, who had been enjoying a quiet start to the game, came to life after 31 minutes with a powerful shot from distance that bounced wickedly in front of Enckelman but the Finnish stopper managed to gather the ball at the second attempt.
The Nigerian international then spurned a fantastic opportunity to break the deadlock when he was sent through one-on-one by Vernon in a quick Dons counter-attack but the winger couldn't keep his composure and fired wide.
Vernon was next to be foiled for the Dons just before the break with his close-range shot from an acute angle hitting the post after Enckelman had kept out Chris Maguire's low drive.
Aberdeen were dealt a major blow within three minutes of the re-start when Northern Ireland international McArdle was shown a red card for a two-footed lunge on Taylor.
Danny Grainger picked up a booking minutes later for a late tackle on Maguire as tempers began to rise amongst both sets of players.
Steven Anderson headed over from a Grainger corner before Aluko skipped past Alan Maybury and unleashed a low shot just wide as both sides continued to search for the opener.
Aberdeen's goalkeeper Jamie Langfield was called upon to make two excellent saves, first in denying MacDonald's acrobatic effort and then to turn Taylor's drive round the post.
The home support were furious when Saints substitute Sam Parkin escaped punishment for an apparent elbow on defender Diamond.
And the Dons defender was cursing his luck after 83 minutes when, under pressure from Parkin, he headed the ball into his own net from MacDonald's cross.
The Dons tried to restore parity in the closing stages with Vernon inches away from connecting with Maguire's enticing cross and substitute Velicka having a powerful strike well held by Enckelman but the visitors held on for a welcome victory.
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