Wes Thomas and Chris Maguire secured Oxford a deserved 2-0 win as Bolton's recent problems continued at the Macron Stadium.
The U's struck twice in the last nine minutes to register their first away win since promotion from Sky Bet League Two.
Bolton have now failed to score in their last four matches and have not won a game since Phil Parkinson was named Manager of the Month for August.
Second best for most of the afternoon, Wanderers failed to seriously test goalkeeper Simon Eastwood despite using six different strikers during the course of the game.
Oxford shaded a dull first half, with Maguire forcing Mark Howard into a scrambling save early on.
Bolton picked up briefly after the break as Charlie Raglan headed Zach Clough's cross from under his own crossbar.
But it was Oxford who made the running late on, Kane Hemmings firing at Howard, who then denied sub Alex MacDonald with another snap shot.
Thomas became the first player other than Hemmings to score away from home for the U's this season with nine minutes left.
And Maguire added insult to injury in the final minute, tapping into an empty net after Howard had palmed away Hemmings' stinging shot.