Struggling Cambridge were quickest out of the blocks and took a first-minute lead when Dunk caught Cobblers cold, beating goalkeeper Matt Duke from the edge of the box.
The visitors went close to doubling their advantage when Nathaniel Mendez-Laing was denied by Duke, who then saved from Ryan Bird.
In-between, James Gray headed over as Northampton tried to get back on level terms but the U’s continued to look the more dangerous side.
They twice went close when Tom Elliott fired over and Ryan Donaldson crashed against the crossbar from the edge of the box.
The Cobblers stepped up a gear as the half progressed, substitute Ivan Toney shot wide from close range and then headed over before Brendan Moloney had a goal-bound shot deflected wide and Joel Byrom fired over from the edge of the area.
Mendez-Laing should have doubled United’s lead straight after the restart but he shot into the side-netting with just Duke to beat.
Toney was denied by former Cobblers keeper Chris Dunn before twice heading over while Lawson D’Ath was off target with two efforts and Moloney had another shot blocked as Chris Wilder’s side went all out for the equaliser.
Substitute Sullay KaiKai missed a great chance late on to seal all three points for United and that nearly proved costly when defender Ryan Cresswell headed wide and Moloney flashed a shot across goal.