Oxford kept up their recent impressive form with their fifth straight win in league and cup without giving away a goal.
After an early strike from Matt Robinson they largely controlled a game which brought them their first win over Rovers in eight meetings.
It was a victory soured by a second-half collision which saw midfielder Dean Whitehead stretchered off.
This was Rovers' seventh league defeat in a row and manager Ray Graydon, who has signed 15 players since taking over in the summer, conceded their season - and league future - is now in crisis.
The breakthrough for Oxford came in the 12th minute when defenders failed to clear their lines after keeper Scott Howie had parried a searching drive from Roy Hunter.
Coming in from the left Robinson's follow-up shot took a deflection to fly past Howie's despairing left hand.
The keeper was soon illustrating Rovers' lack of touch when he put a free-kick straight into touch.
Rovers eventually got their passing game together but with target figure Paul Tait suspended, they had no-one in the air to trouble Oxford's defence.
Their Latvian international Vitalijs Astafjevs had a testing free-kick midway through the first half but Andy Woodman fisted it from under his bar for a fruitless corner.
Astafjevs sparked Rovers' best raid with a direct run but nothing came of it as Kevin Street allowed David Waterman to clear a weak effort off the line.
Oxford's Bobby Ford and Roy Hunter were being given too much freedom to build attacks and three minutes into the second half this midfield superiority was converted into the second goal.
It came though through a bad mistake by Rovers skipper Adam Barrett, who gave the ball away on the byline to Jefferson Louis. The big striker cut back in and at the near post fired between Howie's legs.