But rivals Oxford lost at home to Luton Town and Accrington Stanley drew with Morecambe to hand the Cobblers their first title since the 1986-87 season.
Exeter's Jayden Stockley had a header tipped over the bar before the Bournemouth loanee sent another wide.
Zander Diamond's header was the Cobblers' best effort before Stockley twice hit the bar for the Grecians.
Exeter remain in ninth place, two points off the play-off places.
Northampton Town manager Chris Wilder told BBC Radio Northampton:
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"I don't really know what to say to be honest. I'm taken aback by the reception.
"I think it will be some time until we are able to appreciate just what this group has achieved.
"It is emotional, you work extremely hard to get into a situation like today. To take more than a thousand supporters to Exeter is incredible.
"We've won in all kinds of different ways this season. It just shows the character of these boys and the character of the club."
Northampton Town were crowned champions of League Two, despite being held to a goalless draw at Exeter City.