Both sides had chances in the early stages of the match as Barry Corr tried to head in from a corner for the home side, while Ellis Harrison came close with a long-range effort down the other end after a quick clearance from the visitors.
Corr continued to look the best chance of a goal for Cambridge in the first half, and broke the deadlock just over half an hour into the match when Harrison Dunk curled the ball in from out wide, setting the striker up for a header into the bottom right corner.
Rovers tried to respond at the start of the second half as Lee Brown won a corner when his shot was deflected behind, but Harrison's header from the resulting set piece was kept out by the crossbar.
The visitors continued to enjoy the majority of the possession after the restart, but Jermaine Easter could not beat the keeper with a flick-on from a free kick, while Harrison and Matty Taylor saw further efforts saved.
The pressure paid off with 25 minutes to go though as Harrison was in the right place to meet the ball from a parried effort, hitting it on the half-volley to get last season's Conference promotion winners back on level terms.
Cambridge enjoyed the majority of the possession as the match headed into the final 10 minutes with the two sides still level, but it was the visiting team who broke the deadlock again when Taylor benefited from a quick counter-attack, rifling the ball into the back of the net from the middle of the penalty area.
Taylor had a chance to add his second of the match in stoppage time when Stuart Sinclair curled the ball in from out wide, but a fingertip save prevented the visitors from adding a third.
The result lifts Bristol Rovers up to ninth in the table, while Cambridge sit 14th.