Rovers manager Atkins was making his first return to the Kassam Stadium since leaving the club last March, and he was given a lot of stick from the Oxford fans.
But he must have fancied that the Pirates were on their way back when leading scorer Junior Agogo fired in his 15th goal of the season just 40 seconds into the second half.
Oxford had taken charge with two goals in four minutes early in the game. Lee Bradbury converted a re-taken penalty after keeper Ryan Clarke had brought down Tommy Mooney.
The officials decided that Clarke had moved off his line so ordered the spot kick to be taken again after Clarke saved Bradbury's first effort. And he made no mistake the second time.
Four minutes later centre back Leo Roget headed home Chris Hackett's corner, the ball flying into the net off the head of Robbie Ryan on the goal line.
But Agogo's goal brought Rovers right back into it and in a spell of pressure they went close again when Stuart Campbell fired over the bar and Agogo also headed over.
However, Davies wrapped up the victory for the U's 16 minutes from time with a superb first time finish from Matthew Robinson's cut back.
Although substitute Richard Walker struck a second for the visitors, with a shot over goalkeeper Chris Tardif, it was too late.
Bradbury should have got a fourth for Oxford but after rounding the keeper and two defenders he shot over the bar.
Oxford have now scored eight goals in three straight wins and climbed to 12th in the table, and in Davies, who was this week called up by Wales Under-21s, they look to have an exciting prospect.