Goals from Bradley Dack and Cody McDonald eased Gillingham's relegation fears and kept Tranmere within two points of the League One drop zone.
Rovers are two points above the safety line, while the Gills have moved seven points clear of the bottom four.
Dack superbly volleyed in Joe Martin's deep cross to put the hosts in front with 12 minutes remaining.
And after Tranmere sent keeper Owain Fon Williams forward for a corner, McDonald slotted in to seal the win.
Fon Williams had earlier made a series of saves to keep Rovers in the game, while the visitors close through Jake Cassidy, Jason Koumas and Jean-Louis Akpa Akpro.
Gillingham manager Peter Taylor told BBC Radio Kent:
Post-match: Gillingham manager Peter Taylor
"We needed a very important win and needed a better performance than last Saturday.
"We know what Bradley Dack is capable of - he's got great lungs and legs. At times he's been frustrated that he hasn't played so much lately, but we're happy with his work today.
"We would be unlucky to go down with 51 points, but it's still not impossible so we've got to be careful.
"I spoke to the chairman before - we're not interested in talking about next season, we're just interested in getting enough points to stay up. Once we've got enough points - then Mr [Paul] Scally has got to make a decision."
Tranmere caretaker manager John McMahon told BBC Radio Merseyside:
"It's so difficult to comprehend how we can come away with a 2-0 defeat after that performance.
"Again, a lack of concentration cost us. We gave everything we had and if there was a team that was going to win the game, I thought it was going to be us."
