The League One high-fliers will be the happier of the two sides having played for most of the tie with only 10 players.
Rochdale started brightly with Ian Henderson firing wide and Michael Rose testing goalkeeper Matt Duke. But former Cobblers striker Henderson got a straight red card in the 16th minute for kicking out Ben Tozer.
Despite the setback, Rochdale dominated the first half and created good chances with Matt Lund off target and Matt Done just unable to convert from close range following another good move.
Rochdale went close as the interval approached when Stephen Dawson almost caught out Duke following a poor clearance but his 35 yard lob beat the keeper and hit the bar.
Northampton were completely outplayed in the first half and failed to create a single chance. But shortly after the restart Emile Sinclair finally tested Conrad Logan and substitute Darren Carter’s effort was deflected just past the upright.
But Rochdale still looked the more likely of the two sides to break the deadlock and Duke had to tip over a header from the unmarked Oliver Lancashire.
Ivan Toney had Northampton’s best chances of getting through at the first attempt. He had a couple of headed chances, twice missing the target and then seeing Logan save his second attempt before firing wide late on.
In the closing stages Toney fired over the bar from close range following an excellent cross from Kaid Mohamed.
Both sides went for the winner late on, Cobblers substitute Alex Nicholls was denied by Logan and Ashley Eastham’s header hit the post in the final minute of normal time.