An injury-time goal from Kaid Mohamed saw Morecambe slip to another disappointing away defeat.
In a game of few chances struggling Rovers took the points with virtually the last action of the game when Mohamed was allowed a free header to beat Barry Roche from eight yards out.
The game looked set for a goalless draw but Alex Kenyon failed to clear and with no challenge from Tony Diagne young wide man Alefe Santos sent in a cross which Mohamed finished with a perfect header.
The first half saw few chances with both sides struggling to get to grips with the hard, bobbly rugby pitch.
The Shrimps started the sharper with Andy Fleming drilling a low shot wide from the edge of the box and Diagne lashing an effort past the left-hand post.
The home side began to find some fluency midway inside the half and youngster Santos went close with a shot on the turn just inside the area that ended wide of the left hand post before Mohamed headed straight at Roche from a good opening.
The Shrimps ended the extended first half on top and Jamie Devitt went close with another long-range effort that Steve Mildenhall was glad to see sail past the post.
The second half was another drab affair with no clear cut chances until Mohamed popped up at the perfect time for Bristol Rovers to give their new manager Darrell Clarke a winning start.
Bristol Rovers: Mildenhall, Smith, Brown, McChrystal, Woodards, Lockyer, Santos, Clarke, Beardsley (Harrison 76), Clarkson, Mohamed. Subs not used: Gough, Parkes, Gillespie, Harding, Clucas, Keary.
Morecambe: Roche, Wright, McCready (Hughes 21), Edwards, Threlfall (Ellison 72), Devitt, Fleming, Kenyon, Diagne, Sampson, Amond (Redshaw 62). Subs not used: Arestidou, Williams, Mustoe, Marshall.
Referee: S Hooper