The visitors took a 19th-minute lead when Brian De Keersmaecker delivered a curling free-kick from the right and Nik Prelec timed his run perfectly to power a header past goalkeeper Radek Vitek from a central position just outside the six-yard box.
It was 2-0 in first-half stoppage time as a hotly-disputed corner from the right was cleared into the path of Przemyslaw Placheta, whose sweetly-struck left-footed shot from 25 yards found the top corner.
Anis Mehmeti matched Placheta’s effort with a brilliant right-footed strike from distance for City in the 53rd minute, which went in off the underside of the crossbar.
But the final minute of normal time saw De Keersmaecker send another free-kick into the box from the left and Greg Leigh claim the faintest of touches off his head as the ball curled past Vitek.
City were unchanged from the 3-0 win at Sheffield Wednesday in their previous game, but had to make a switch after just 15 minutes when centre-back Rob Atkinson was forced off by injury and replaced by George Tanner.
Oxford had made the faster start, with Prelec, making the first start of his season-long loan from Cagliari, denied by a smothering save by Vitek after five minutes. Sam Long fired over from distance as the Robins were hurried into passing errors.
Ross McCrorie headed over for the hosts and Emil Riis shot high and wide from a Mehmeti pass before Prelec broke the deadlock. But Vitek was in action again to save a Will Lankshear volley as Oxford continued to threaten.
Long produced a goal-saving tackle to deny Mehmeti a 26th-minute equaliser and Brodie Spencer cleared an inswinging corner off the line to the delight of Oxford fans. Then Riis shot wide when put clear by a Rob Dickie through-ball.
The dangerous Placheta caused City problems down Oxford’s right and it was fitting that he should have the final say of the first half with a stunning strike.
It was so nearly 3-0 after 51 minutes when Long leapt to meet a right-wing corner and saw his downward header hit a post before being cleared. Mehmeti’s wonder striker two minutes later came just in time to rouse Bristol City fans starting to doubt their team.
Adam Randell sent a shot fizzing inches wide in the 66th minute with the home side on top. Both managers then made multiple changes and one of Oxford’s substitutes, Stanley Mills, brought a diving save from Vitek with his first touch.
Home supporters in a 23,440 crowd did their best to lift City, but Oxford dug in impressively and were well worth the points, with substitute Leigh sealing victory at the death.