Craig Disley headed an injury-time winner to snatch victory and condemn Millwall to their eighth home defeat of the season.
In a dour encounter it always looked as if one goal was going to settle matters, and when Lewis Haldane worked an opening in the 91st-minute, there was Disley to send his glancing header creeping in off the far post.
It was an afternoon of abject misery for Millwall, who were dealt a blow before kick-off when striker Lewis Grabban was ruled out with a groin injury.
Boss Kenny Jackett started with Jay Simpson up front alongside Gary Alexander and Ahmet Brkovic slotting in on the right.
Rovers could have been forgiven for having one eye on next weekend's FA Cup Quarter Final against West Brom, but they certainly didn't play like it.
The visitors matched The Lions stride for stride and effort, but the game never really took off as a spectacle.
Zak Whitbread's fifth minute header from a Dave Martin was blocked on the line and then Simpson's low shot from a Gary Alexander flick-on was comfortably held by Steve Phillips in the Rovers goal.
Millwall should have been awarded a penalty on 27 minutes when Ali Fuseini broke into the area, and despite having his shirt pulled back, kept his balance, only to be denied by a brilliant block by Phillips.
Five minutes later a Brkovic freekick was only half-cleared, Marcus Bignot picked up the loose ball and dinked in a cross that Whitbread met, only for keeper Phillips to pluck the defender's goalbound header out of the air.
Lions boss Jackett made a double substitution just before the hour to try and spark his side into life, introducing Ryan Smith and Adrian Forbes for Brkovic and Martin.
The home side did get the ball in the back of the net on 73 minutes when Alexander powered a header home from Danny Senda's cross, only for his effort to be ruled out for offside.
Rovers rarely threatened throughout, but when Rickie Lambert burst clear in the 80th-minute he looked odds-on to score but keeper Evans and then skipper Paul Robinson combined to thwart the frontman.
The next time Evans handled the ball was to pick it out of the net in injury-time when Disley's header caught the keeper flat-footed and the ball squeezed in at the far post.
It was a shattering blow for The Lions, but one they cannot afford to dwell on with successive away games at league leaders Swansea City and then Yeovil Town, who like Hartlepool, are too close to the relegation pack for comfort.

Millwall: Evans, Bignot, Senda, Fuseini, Robinson, Whitbread, Martin (Smith, 58mins), Alexander, Brkovic (Forbes, 58mins), Simpson, Laird. Subs not used: Edwards, Frampton, Dunne.

Bristol Rovers: Phillips, Lescott, Hinton, Coles, Jacobson, Lines, Campbell, Disley, Igoe (70mins), Lambert, Williams (Rigg, 64mins). Subs not used: Anthony, Pulis, Klein-Davies.
Scorer: Disley (90+1mins)

Ref: Richard Beeby
Att: 9,202 (away 600)