Pearson's strike earned the Robins their first victory in six matches and denied Southampton the chance of extending their three-point lead at the top of the Championship.
Saints failed to convert possession into clear-cut chances and could have lost by more than one goal if Nicky Maynard's 53rd-minute effort had not been ruled out for offside.
The victory for Derek McInnes' side sees them move three points clear of the bottom three, while Southampton's 2011 unbeaten home league record was ended in their 50th and final league match of this calendar year.
After a scrappy opening to the contest, Steve De Ridder raced down the right wing and after pulling the ball back to Rickie Lambert, the striker failed to manoeuvre an effort on target.
Midfielder Jack Cork shot over from 25 yards as Saints tried to stamp their authority on the game, before Albert Adomah also failed to direct his shot on target for the visitors.
Morgan Schneiderlin drove through the midfield region and tested former England goalkeeper David James, who had to tip the long-range strike over the crossbar.
From the resulting corner, Lambert rose high at the back post but could only head over.
Adomah continued to be a constant threat on the break, stealing the ball off Adam Lallana before unleashing a shot that Kelvin Davis smartly turned around the post.
As the game started to open up De Ridder almost brought the first goal, James having to smartly tip the midfielder's effort to safety.
The game sparked into life eight minutes after the interval when City thought they had taken the lead.
After Davis parried Kalifa Cisse's strike into the path of Maynard, the highly-rated striker converted the rebound neatly but was deemed to be in an offside position.
Southampton restarted quickly and had chances of their own, Guly Do Prado and Cork both firing over from the edge of the box.
The Robins were close to going in front again through Pearson after 73 minutes. The midfielder got in round the back of the home defence but his weak effort was kept out by Davis.
James had to be alert again at the other end, keeping out a fierce Lambert strike, while Lallana saw a shot deflected just wide.
Pearson did go one better five minutes later, tapping in after Davis had blocked efforts from Cole Skuse and Maynard.
Southampton tried hard to find an equaliser, Do Prado failing to hit the target again and Lambert trying in vain to win a penalty after he went to ground in the area.