Goals by Andy Kirk and Bradley Johnson in the final ten minutes of the first half gave the Cobblers a cushion they held until injury time when the Quakers leading scorer, Tommy Wright, mirrored home counterpart Kirk by grabbing his tenth goal of the season.
It was too little too late for Darlington and, really, the home side should have put it beyond recall with both Poul Hubertz and Kirk striking the woodwork.
Northampton went in front in the 35th minute when David Stockdale failed to hold a cross from Jason Crowe and Kirk gleefully stroked the ball home through the surface water.
Six minutes later Johnson struck his third goal of the campaign with a sweet left-footed strike into the far corner from the edge of the box.
There was still time before the break for Hubertz to hit the post with a snapshot on the turn and he also went close after the break, volleying over the crossbar after a clever lob had put him clear of the visiting defence.
Darlington were much livelier after the break and signalled their intent with a 35-yard screamer from Wright which flew over.
There was extravagance at both ends with Colin Larkin firing over in the 59th minute when the ball fell neatly into his path, while Johnson missed a great chance to bag a second after racing clear on to a Crowe throughball.
Darlington grabbed their consolation in injury time when a cross from Ricky Ravenhill was headed in by Wright.