They missed the game after being suspended by the club who tried to plug the gap with two young reserves borrowed from Charlton.
Looking for their first win in eight games, Tranmere for a long time thought this could be their day as they put a reshaped home defence under pressure.
Only a great diving save by Steve Phillips from Chris Greenacre kept them from going in front just before half time.
The shot bypassed a crowded area and looked certain to finish in the bottom left-hand corner of the goal until the keeper somehow fisted it out.
The Wales coach John Toshack was in the ground to check out David Cotterill who he turned into the youngest ever full international a few nights ago.
Cotterill was forced to vacate his usual place on the right in the enforced reshuffle to fill in on the left.
He was still the pick of a City attack for the first hour, although was inclined to over work the ball.
One of his shots rattled Tranmere as it flew outside the far post and another bounced off the chest of keeper John Achterberg.
City were forced into an early change after the break when Kelly Youga, one of their Charlton loanees, limped away with a groin strain.
While they were adjusting to the injury City were grateful to Phillips for another notable save from Delroy Facey.
But the deadlock was broken after 65 minutes by Luke Wilkshire.
The Australian emerged from a quiet first half with a run and a cracking shot which came back to him off the bottom of the post. His follow up shot was spot on although Achterberg did get a hand to it.
It was Tranmere's fourth defeat in a row and their fifth visit to Ashton Gate without scoring.