Hasney Aljofree and Andy Nicholas both returned to the starting line up after injury, and Barry Corr was on the bench having also returned from injury.
Both teams started slowly, but only having a handful of chances in front of goal. Swindon's best chance fell to Lee Peacock mid way through the first half, but the Tranmere 'keeper saved it.
The game seemed to he heading towards a 0-0 with the defence for both sides keeping shots to a minimum, before Barry Corr was bought on with 9 minutes to go replacing Billy Paynter.
Barry Corr gave Swindon the lead late on after 88 minutes when he just managed to reach the ball and from close range scored to make it 1-0.
Overall both sides did well, and a draw would also have been a fair result, but a win was good for Swindon who move back up to 7th in the League One Table ahead of next Saturday's away trip to Port Vale.