Dany N'Guessan's penalty claimed a 1-0 victory for Swindon which condemned Tranmere to a fourth straight league defeat.
Frenchman N'Guessan scored his third of the campaign from the spot just before the half-hour mark after Alex Pritchard was brought down by Tom Hateley.
Mark Cooper's Robins, now unbeaten in their last five league home games, controlled the first half from the off but struggled to break down their dogged opponents.
After Nathan Byrne and Nile Ranger had failed to open the deadlock, an uneventful opening 45 minutes only sparked into life when former Millwall player N'Guessan sent Owain Fon Williams the wrong way from the spot.
Rovers, who are in the relegation zone having only won once all season, responded well and almost went into the break on level terms but Liam Ridehalgh saw his 43rd-minute drive was well saved by Wes Foderingham.
Ronnie Moore sent his Rovers side out to attack in the second period but it was the hosts who looked the most likely to score and would have doubled their lead but for a fingertip save from Fon Williams to deny Massimo Luongo late on.