Town were content to play on the break even after teenage winger Craig Nelthorpe had fired Doncaster Rovers into a 13th minute lead.
It came not long after Sean Thornton had gone close with a dipping 20-yard free-kick that was only inches over the crossbar.
Nelthorpe hit the mark with his first league goal, firing home with his left foot after James Coppinger had set up the chance.
Doncaster should have had a penalty when star-man Coppinger was sent sprawling in the 25th minute. But the referee, whose overall performance left much to be desired, waved away the appeals.
There was a scare for Doncaster in the 38th minute when goalkeeper Jan Budtz kicked the ball straight at the feet of Holt, but the Northampton wing-back could only fire into the sidenetting from an acute angle.
The Cobblers hit back to equalise deep into first-half stoppage time when Jason Crowe fired home following a goalmouth scramble after Holt had launched the ball into the box.
Rovers continued to dictate the pace in the second half and Coppinger was unlucky not to score when he hit a fierce shot goalwards, only to see Mark Bunn make a fine save at full stretch.
But there was no stopping Gareth Roberts in the 59th minute when he slammed the ball home from the edge of the box for his first goal for the club after Mark Wilson had set up the chance.
Holt came to Town's rescue again five minutes later with another long throw that led to skipper Mark Hughes cashing in on some slack defending when he headed home from close range.
Bradley Johnson hit the post following a breakaway attack from Northampton nine minutes from time, but it would have been a travesty had he scored, but Doncaster only had themselves to blame in a match they should have won.