Derry were by far the better side in the first half but Rover's produced the goals in the second half.
Ronan Finn gave Rovers the lead on the hour mark while the second came nine minutes later from Dean Kelly.
Derry will feel they should have had more out of the game.
The result brought the Candystrips six game unbeaten run to an end.
The points difference between the hoops in 4th and Derry in 5th is now out to 13 points.