City suffered their first home defeat of the season with Corey Blackett-Taylor’s late goal proving the difference between the two sides.
Despite having the better of the game throughout the 90 minutes, Blackett-Taylor’s strike, against the run of play, handed Tranmere the three points with the visitors only shot on target.
The Sky Blues created the first chance of the match after just four minutes when Liam Walsh’s lofted through pass was met on the volley by Jordy Hiwula but could only find the roof of the net from six yards out.
The visitors then carved out a chance of their own, minutes later, with Darren Potter dragging an effort well wide of the target from the edge of the penalty area.
After a quiet opening half an hour, Hiwula was next to test the Tranmere goal when his low drive from 25-yards out was deflected past the post.
City then came within a whisker of taking the lead just before half time when Callum O’Hare’s deflected cross was inches away from the head of Matty Godden.
Moments later, Godden came close again, flashing Fankaty Dabo’s cross from the right wide of the near post.
HALF-TIME: SKY BLUES 0-0 TRANMERE ROVERS
City continued to search for the opening goal five minutes into the second half when Godden fired a first-time effort over the crossbar after some tidy play from Zain Westbrooke.
Dabo continued to cause Tranmere problems down the right-hand side and produced another excellent cross that was once again met by the head of Godden with the ball sailing just wide of the left-hand post.
Godden was in the thick of the action again just a minute later when he was slipped through on goal by Jordan Shipley, with his low curling effort beating Scott Davies only to come back off the post.
The Sky Blues dominance continued just past the hour mark when Shipley this time played in Hiwula down the left-hand side of the penalty area with the forward flashing an effort wide of the post from close range.
Tranmere took the lead against the run of play on 83 minutes, when Blackett-Taylor finished into the right corner of the goal after running onto Kieron Morris’s flick on.
The visitors almost scored a second goal in the final minute of normal time with Stefan Payne firing wide from close range.
With the clock ticking, substitute Gervane Kastaneer tried his luck from distance but could only blaze his effort over the crossbar.
FULL-TIME: SKY BLUES 0-1 TRANMERE ROVERS
Goals: Blackett-Taylor (83’)
Yellows: Payne 38’, Dabo 39’, Hepburn-Murphy 59’, Davies 70’
Sky Blues XI: Marko Marosi (GK), Fankaty Dabo, Dom Hyam, Michael Rose, Sam McCallum (Mason 77’), Liam Walsh, Zain Westbrooke (Bakayoko 82’), Jordan Shipley, Callum O’Hare, Jordy Hiwula (Kastaneer 71’), Matty Godden (C)
Unused Subs: Ben Wilson (GK), Tennai Wilson, Morgan Williams, Liam Kelly
Tranmere Rovers XI: Scott Davies (C) (GK), Jake Caprice, George Ray, Manny Monthe, Liam Ridehalgh, Kieron Morris, Darren Potter, Harvey Gilmour, Corey Blackett-Taylor, Paul Mullin (Hepburn-Murphy 34’), Stefan Payne
Unused Subs: Luke Pilling (GK), Sid Nelson, Cameron Borthwick-Jackson, Kane Wilson, Carl Spellman, Danny Walker-Rice