Antony Evans came off of the bench to score a 75th-minute penalty for the Gas to take home three points.
Rovers - playing their game in hand - moved up to 15th as a result of their win and play Cheltenham Town on Saturday.
Dons suffer their fifth sefeat in six matches with Liam Manning’s side 22nd in the League One standings.
Tale of the match
Bristol Rovers started on the front foot as they looked to make the most of Dons’ lack of confidence given their one win in five league matches.
Lewis Gibson caught a shot nicely outside the box but volleyed just wide of the target after Paul Coutts’ second set-piece delivery.
Two yellow cards were shown in quick succession as Aaron Collins was booked for a foul and then Dan Harvie went reckless on him moments later.
Luke McCormick almost opened his account in his second spell but the midfielder’s low shot bobbled wide of the post.
A ball across goal from Collins was almost touched home by Ryan Loft but the striker was just yards from stroking home. It was an otherwise quiet first period with the away side on top with the better share of shots.
Dons showed more about themselves in the second-half as James Belshaw had to hold on to Bradley Johnson’s header from Hardie’s cross.
Ryan Loft got Rovers’ best chance as Coutts picked off a loose ball and passed it to the striker to let fly from 20-yards, forcing Jamie Cumming to dive down.
After earning a foul from Zak Jules on the edge of the box, Collins’ stepped forward to take a free-kick. His attempt deflected over the bar in another near moment for the men in black.
A finger-tip save from Cumming was from Rovers best chance as Gibson powered a header amongst a sea of bodies.
Chances continue to come for Rovers as Rossiter drove a shot just past Cumming’s goal in an attacking spell for the visitors.
Their patience paid off as Loft was manhandled in the penalty box and a spot-kick was awarded. Substitute Antony Evans stepped forward and drove his penalty home with 15 minutes remaining.
Despite six minutes of additional time, Rovers had no threat on Belshaw’s goal with home fans booing at the full-time whistle.
James Belshaw - 7
Routine performance. No major problems for the Rovers goalkeeper from the home attack.
Lewis Gordon - 7
Down both flanks, Rovers wanted to attack down the left and Gordon helped the team get forward. A solid defensive performance.
Bobby Thomas - 7
Another appearance for Thomas who is one of the more consistent figures in the team.
Lewis Gibson - 7
Interesting choice to start after Hoole’s performance on Saturday but the on-loan Everton defender didn’t put a foot wrong.
James Gibbons - 7
Another few minutes in the locker for Gibbons who ground out a solid performance.
Luke McCormick - 6
He showed a few glimpses in the first-half and had a good chance. An hour in his locker will do him some good which will have been the plan.
Paul Coutts - 8
A surprise inclusion given Sam Finley was named man-of-the-match on Saturday. He was good with his set-piece delivery and delivered an assured performance in the centre. Intercepted play and got Ryan Loft in to play.
Jordan Rossiter - 7
Another good performance from Rossiter who dealt well with a change of two midfielders pre-match. He has really looked the business in the past few months.
Aaron Collins - 7
Quick-footed. A handful for the Dons defence from all angles as he found joy on his flank, as well as from dead ball situations. He just needed the strikers to anticipate his service. Another solid shift from the Welshman.
Josh Coburn - 6
Fed off scraps but an otherwise quiet night in front of goal for the striker. An hour or so or of competitive football will do him well
Ryan Loft - 7
Won the penalty that ultimately won the match for Rovers. He had a few chances here and there but did the dirty work as a striker. Committed to the cause.
Sam Finley (subbed on, 61) - 6
A superb back-tracking challenge as soon as he entered the pitch to get Paul Coutts out of trouble.
Antony Evans (subbed on, 70) - 7
Calmness personified. Five minutes after coming on, he came on and slotted away a powerful penalty. He almost returned the favour by picking up a loose ball and
Luca Hoole (subbed on, 70) - 6
Came on in a like for like substitute and did his job. Right-sided defender in a four is where his role is
Harry Anderson (subbed on, 83) - 6
A moment of brilliance in stoppage-time with Anderson shielding the ball from his opponents, earning an applause from the Rovers fans in the corner.