Accrington's defence was waiting for the off-side flag in the 90th minute when Jean-Louis Akpa-Akpro's pass found Ryan Lowe with only keeper Marcus Bettinelli to beat, but it did not go up and the experienced striker finished in style.
It was hard on Stanley, who created the better chances in the opening half-hour with Tranmere keeper Owain Fon Williams having to be at his best.
James Gray had the first chance, clipping the ball just over the crossbar, while Kal Naismith's strike was saved by Fon Williams.
The keeper was in the action again soon after when Kayode Odejayi raced clean though, but the striker tried to take the ball around the keeper and Fon Williams got a hand to it.
Peter Murphy then fired just wide, Naismith forced another save out of the Tranmere keeper and Gray was not far off with a long-range effort.
The League One side did have a couple of chances before half-time through Chris Atkinson and Jake Kirby, while Lowe did have the ball in the back of the net, but it was ruled out for off-side.
Both sides struggled to create clear-cut chances in the second half with neither keeper seriously troubled.
Rovers substitute Akpa-Akpro had a chance in the final 10 minutes, but headed wide before Lowe's late show.