The home side were booed off at the interval after a disjointed first-half display saw Tranmere take control.
They took the lead on 25 minutes when Shane Sherriff's low cross was deflected in following a free kick on the corner of the box.
Just before the break Paul McLaren latched onto a mistake by City midfielder Cole Skuse before lashing a low drive past Adriano Basso with the help of a deflection.
City had missed a couple of first-half chances, with Phil Jevons the culprit. But they had created precious little against well organised and hard working opponents.
That all changed following a half-time tongue lashing from manager Gary Johnson. His team emerged far sharper and worked a lot harder than they had done in the first period.
Tranmere goalkeeper Joe Hart looked at fault on 49 minutes when Enoch Showunmi headed in from almost on the goal line following a short corner.
That transformed the game and City were level on 58 minutes when a Stephen Brooker shot was blocked and the ball ran to Jevons who fired low past Hart from 12 yards.
Tranmere were visibly shaken and brilliant work by Brooker set up the winner on 68 minutes.
His chip from the edge of the box bounced back off a post into the path of substitute Jennison Myrie-Williams who tapped home the rebound to score with his first touch.
The young winger had replaced Bradley Orr less than two minutes earlier, while at the same time Johnson introduced Brian Wilson, his new signing from Cheltenham Town, in place of Jevons.
Tranmere created a few second half chances, but couldn't take them. It was a frustrating day for the visitors who looked so controlled for 45 minutes and so vulnerable in the second half.
City are proving comeback experts this season. Manager Johnson reckoned it was the sixth time they had come back to win or draw from being behind.
He will be wondering how to get his players into top gear before they concede the opening goal, but could have no complaints about the spirit in the side and their sparkling football after the break.