Frustration for Latics
They had plenty of chances, but were unable to find a route to goal.
And they lost to an injury-time goal, a penalty from Tranmere substitute Ryan Lowe.
Latics made a double substitution in the 63rd minute in a bid to break the deadlock as Albert Rusnak was handed his debut and Anton Rodgers also brought on. They replaced Jonson Clarke-Harris and James Wesolowski.
And former Slovakia under-18 captain Rusnak (pictured) almost made a dream start but his header from Sidney Schmeltz’s cross was comfortably caught by keeper Owain Fon-Williams.
Manager Lee Johnson made his third and final change with 15 minutes left as Cristian Montano came on for James Dayton.
Tranmere came close to snatching an 82nd minute lead when a header from defender Ash Taylor flashed just wide of the upright.
Fon-Williams had to be alert to turn over a shot from Montano as Latics looked to break the deadlock.
But it was Rovers who snatched the points when they won a 93rd minute penalty after keeper Mark Oxley was adjudged to have brought down Lowe.
Lowe picked himself up to score from the spot as Rovers snatched victory in the fourth and final minute of stoppage time.
Full-time: Latics 0, Tranmere Rovers 1.