David Lee and Tony Kelly’s team had already notched a friendly win against Preston since returning to action a week earlier.
But this was a second successive win in the FA U18 Premier League.
The young Whites took the lead in just the 11th minute when a ball in from the left found Christopher Cvetko in space on the edge of the box and he fired home.
Rovers drew level midway through the first half when Sam Joel fed Yeray Torres and he finished with aplomb past Whites stopper Harry Campbell.
Level at the break, it was Wanderers in the ascendancy again at the start of the second half and they edged ahead again on 57 minutes when Cvetko scored his second with a low drive from 18 yards.
Ten minutes later, however, Rovers were level again when George Pierce steered home a shot.
Lee and Kelly’s side were not done, though, and sealed the points when two substitutes combined for the winner in the final minute of the 90.
Jamie Hinchcliffe crossed from the right and Guillermo Torres was on hand to convert.
It was a victory that pleased Lee who said: “We started the game very positively, having the better of the play.
“We created several early chances, before Christopher Cvetko opened the scoring with a great low strike from the edge of the box.
“We were pegged back twice, but at 2-2 we took control of the game and deserved to win.
“It was a very good all-round performance.”
The U18s will go for a hat-trick of league wins back on home turf at Lostock on Saturday when they host Everton, kick off 11am.