The promotion-chasing Cobblers had won nine of their last 10 games at home while improving Rovers had lost just once in seven games and it was John Ward's men who looked the more likely to claim all three points for long periods.
Rovers survived Northampton's early threat from set-pieces with Clive Platt going closest to breaking the deadlock with a header. Adebayo Akinfenwa also had a close-range effort blocked on the line before seeing Steve Mildenhall gather his header at the second attempt.
At the other end Joe Anyinsah tested Lee Nicholls with a low drive and Oliver Norburn forced the Cobblers keeper into a smart save at his near post.
Rovers continued to frustrate Northampton after the restart as the hosts struggled to create openings. The visitors grew in confidence and began to dominate the second half while denying the Cobblers any real chances.
Eliot Richards twice fired in low drives which Nicholls did well to keep out and skipper Tom Parkes volleyed wide. But with just two minutes left, Harding volleyed home from close range after Clarke Carlisle helped on Ben Tozer's long throw-in.