Battling Cheltenham did not make life easy for them and were down to ten men at the time of the opening goal. James Wesolowski was receiving treatment and in fact did not return.
There were few chances in the opening period. One of the best fell to Andy Lindegaard in the fifth minute, but his close-range header from a Lee Ridley cross was turned away for a corner by home keeper Danny Coyne.
Tranmere were again slow to start, but as they warmed to their task Steve Jennings blazed over and a low drive by Gareth Edds was well held by Scott Brown.
Andy Taylor just missed the target with a well struck angled free-kick and then Ian Moore had no better luck when set up by Savage.
It was mainly low-key entertainment at this stage for the sparse crowd, before Wesolowski volleyed wide for Town just before the break.
Drissa Diallo was excellent in the back four for the visitors and Lindegaard was busy in midfield but there was a lack of bite up front
Skipper Antony Kay tried hard for the Merseysiders and Savage and Chris Shuker were often in the thick of the action.
Coyne pushed over a Lindegaard lob soon after the re-start but most of the pressure came from Tranmere.
Kay missed the target, then Scott Brown in the Town goal did well to turn away a deflected shot by Taylor.
Next it was Shuker to let fly and the ball sailed just outside the right-hand post.
But the breakthrough came as Savage headed in at the far post from a Shuker cross.
Shuker almost made it 2-0 in the 87th minute but his effort rebounded off a post. However, two minutes later sub Sonko headed in with Shuker again the creator.