The Sky Blues were not able to make it three wins from three at the Memorial Stadium as an impressive 15 minutes from the home side was enough to see off City.
The Sky Blues began the game on the front foot, carving out a number of chances in the opening couple of minutes.
City's first chance fell to Jordan Shipley on the edge of the box as Dom Hyam nodded down Doyle's deep corner kick. Shipley set himself and unleashed a half-volley goalward but his effort was matched by Bonham who tipped the strike over the bar.
Soon after, it was Thomas who spurned a chance as Chaplin's deep cross found the winger unmarked at the back post. Thomas took a touch and fired towards goal, but his effort skimmed just wide of the far post.
City were soon regretting their missed chances as Gavin Reilly was sent clean through on goal with just Burge to beat. Burge came out diving towards the Rovers man's feet but Reilly was composed enough to slot the ball underneath the on-rushing 'keeper.
The home side had their tails up and their lead was nearly doubled minutes later. The ball fell to Stuart Sinclair on the edge of the box and his shot was destined for the back of the net but for Hyam who stood tall and deflected the ball away from goal.
But it did not take long for the Pirates to double their lead as Tom Lockyer came in at the back post and headed past Burge from an in-swinging corner.
The Sky Blues were looking to gain a foothold in the game but Rovers kept attacking, and soon they had found their third goal. A Rovers cross was directed away from goal but for Ollie Clarke to pick up the loose ball, gain a yard of space and unleash a rocket into the top corner, stinging the palm of Burge on its way in.
The pressure from the home side began to slow and City played their way back into the game despite the goal deficit. Chaplin tried his luck from range following a neat turn to escape his defender, yet his effort flew wide of the goal.
The Sky Blues then went on to control the balance of play for the rest of the half, completing 41 passes in total in one move. The move was finally interrupted by a foul on Chaplin 40-yards from goal. Doyle stepped up and delivered a floated cross to the back post for Hyam to head emphatically into the back of Bonham's net, and give City a slither of hope going into the second half.
HALF-TIME: Bristol Rovers 3 - 1 Sky Blues
The Sky Blues came out for the second half in a similar vein to how they ended the first. They had the bulk of possession - but not for lack of trying - could not manage to breach the Pirates defence once again.
Neither side managed to create any clear-cut chances within the first 20 minutes of the second period, but it was City who came closest to finding the back of the net via Jonson Clarke-Harris. Hyam headed the ball back across goal from Doyle's deep corner-kick and Clarke-Harris rose highest but headed inches over.
The biggest shout for the home side came when Jordan Willis appeared to have handled the ball in the penalty area, but the referee waved play on.
With 20 minutes still left to play, City were still chipping away at the Pirates' back line, and Conor Chaplin found himself in behind the defence following a long ball out from the back. With the angle narrowing at every moment, Chaplin did well to get his shot off as the ball was skipping along the greasy surface, but the on-rushing Jack Bonham was equal to his effort.
The Sky Blues did have the ball in the back of the net with just minutes from time following a smart finish from Chaplin. However, as he looked across at the linesman as he wheeled away in celebration, the flag went up for offside.
FULL-TIME: Bristol Rovers 3 - 1 Sky Blues
Sky Blues XI: Lee Burge (GK), Dujon Sterling (46), Dom Hyam, Jordan Willis, Junior Brown, Michael Doyle (C), Liam Kelly (70), Jordan Shipley, Luke Thomas, Jonson Clarke-Harris (84), Conor Chaplin
Subs: Liam O'Brien (GK), Jordon Thompson (46), Tom Davies, Abu Ogogo, Tony Andreu (70), Jordy Hiwula, Amadou Bakayoko (84)
Bristol Rovers XI: Jack Bonham (GK), Tom Lockyer (C), Tony Craig, Ollie Clarke, Tony Nichols (57), Chris Lines, James Clarke, Gavin Reilly (73), Kyle Bennett, Stuart Sinclair (82), Michael Kelly
Subs: Adam Smith, Daniel Leadbitter, Ed Upson, Stefan Payne (57), Tom Broadbent, Alex Jakubiak (73), Sam Matthews (82)
Goals: Gavin Reilly (7), Tom Lockyer (19), Ollie Clarke (22), Hyam (45)
Attendance: 8,385 with 1,137 travelling Sky Blues.