Wanderers saw their six-game unbeaten run come to an end as they missed an opportunity to put pressure on the teams above them in the top six, writes Pete Oliver.
The Whites twice fought back from a goal behind and should have had something to show for an outstanding first-half performance.
But they failed to take further chances at critical moments to add to goals from Aaron Morley and John McAtee either side of half-time.
And in a wide open second half, Steven Shumacher’s men then conceded a late goal to suffer a first league defeat since the head coach’s first game in charge as his side remained in the final play-off berth – two points behind Saturday’s opponents Stockport County.
Wanderers boasted an impressive record at the Memorial Stadium with four successive wins and no defeat in five visits stretching back to 1989.
But having scored the opening goal for the first time under Schumacher in Saturday’s win at Burton Albion they reverted to recent type by conceding first again to go behind to an early penalty.
Alex Murphy, playing as a left-back behind the returning Szabi Schön with Gethin Jones also back in the team on the opposite flank in a four-man defence, was too ponderous in dealing with a ball into the box and then fouled Kofi Shaw as he looked to recover.
Chris Martin slotted home the spot-kick with just six minutes gone to give Rovers, seeking a fifth win in seven home games, the ideal start in their bid to keep pulling away from the relegation places.
That didn’t set the tone, however, as Wanderers – wearing an all-white kit – responded impressively as they tried to engineer another fightback.
Josh Sheehan was often the orchestrator and from one of his sumptuous passes Schön delivered a near-post cross George Thomason steered wide.
And with Wanderers by far the superior side it looked only a matter of time before they would equalise as they opened Rovers up at will down the flanks.
Aaron Collins missed a great chance to score against his former club after Jones had cushioned a Murphy cross into his path and seven minutes before half-time the pressure did pay off when Morley made it 1-1.
The midfielder was enjoying another magnificent game and when a corner reached him beyond the far post, he drilled a clinical strike through a crowd of bodies and into the back of the net to claim his third goal in five games.
All the momentum was with Wanderers but in an untidy start to the second half they allowed the hosts to build up a head of steam and it needed a superb save from Luke Southwood to keep out an effort from Ruel Sotiriou before the Whites’ keeper also denied Shaw in an anxious few minutes.
The pressure should have been short-lived, however, as Wanderers suddenly had two outstanding chances to go in front and regain control but McAtee steered his attempted finish wide and Schön somehow failed to convert a driven cross from Sheehan.
The goals at both ends were living a charmed life as Gas forward Sotiriou was then sent clear but clipped his effort inches wide in a frenetic spell and Wanderers didn’t heed the warning as they then went behind for a second time with 63 minutes gone.
Again Sotiriou got away and this time he picked out Martin with a low cross for the striker to pick his spot and slot home his second of the game.
That left Wanderers with it all to do once more and, again, they found a way to bounce back as McAtee met another Morley corner with a near-post header he glanced into the net to claim his 12th goal of the season.
With multiple substitutions and Schumacher using all his attacking options both sides went for a winner and with a couple of minutes to go it was Rovers who got it.
Wanderers conceded one set-piece too many and when the ball reached Connor Taylor at the far post, the big defender nodded in to end Wanderers’ unbeaten run in disappointing fashion.
Wanderers: Southwood; Jones (Randall 83), Toal, Forrester, Murphy (Mendes Gomes 68); Sheehan, Thomason (Forino 83); McAtee, Morley, Schön (Osei-Tutu, 59); Collins. Substitutes: Baxter, Lolos, Matete.
Booked: None
Bristol Rovers: Ward; Wilson, Taylor, Swinkels; Moore (Thomas 83); Senior (Hutchinson 77), Shaw, Butcher, Mola (Sousa 83); Martin (Sinclair 71), Sotiriou. Substitutes: Hall, Dewsbury.
Booked: Swinkels, Forde
Referee: Carl Brook
Attendance: 7,644 (939 Wanderers)