The on-loan Peterborough forward nodded in Scott Kerr's 80th-minute corner from barely three yards out as all the Oxford defenders stood staring at floundering keeper Billy Turley.
The Red Imps deserved the victory as they just shaded an uninspiring game.
They hit the woodwork twice, while Oxford also hit the bar.
The visitors' Gary Birch nodded a Kerr free-kick against the crossbar in the 13th minute.
They then went close again with giant centre-back Jamie McCombe heading a corner narrowly over.
Oxford's on-loan Brentford striker Scott Fitzgerald shot against the post after a driving run from Lee Mansell.
But seven later City's Lee Beevers hit the bar at the other end with a scooped shot when a free-kick from the left came over.
It was Oxford's third straight home defeat in league and cup and they were watched by their lowest-ever league gate at the Kassam Stadium 3,795.