And the recovery owed to the injustice they felt when Oxford opened the scoring on 58 minutes when Tommy Mooney knocked in a Craig Davies' right-wing cross at the far post for his ninth goal of the season.
The Cobblers were convinced that Chris Hackett had dived in the build up to the goal and their players stood like statues waiting for the referee to blow his whistle.
They protested angrily after the goal was given and goalkeeping coach Dave Watson was sent to the stand for his protests.
Fired up, they hit back six minutes later with Eric Sabin knocking the ball into an empty net from 18 yards after Oxford keeper Chris Tardif failed to punch clear in the windy conditions.
Oxford had barely recovered from that equaliser when Northampton struck again. This time Scott McGleish was in the right place to bury a low drive past a defender and Tardif on the goal line from 16 yards.
Northampton completed the double over Oxford but they were indebted to two brilliant saves in quick succession from Lee Harper.
In an astonishing spell of action, Harper tipped Leo Roget's header onto the bar, Mateo Corbo then had a follow up effort headed off the line by Christopher Willmott and then Harper tipped over another effort from Matthew Robinson who was also following up.
From the corner, Jamie Brooks drove through a crowd of players but Harper saved again.