Town knew two wins from their final two games would guarantee a top three finish but Sam Nombe cancelled out Mitch Pinnock’s brilliant first-half strike to open the door to Port Vale and Mansfield Town, both of whom play on Monday.
Jon Brady’s side do remain third in League Two for now, above Bristol Rovers on goal difference, and they are also assured of a play-off place at the very least due to Sutton’s defeat to Bradford.
Saturday's contest at Sixfields was an entertaining game between two good sides and Cobblers did look on track for a huge victory through Pinnock's superb finish, but a bad miss from Josh Eppiah in the second-half proved costly as Exeter swiftly equalised to go top of the table.
For the fourth game in a row Brady picked the same starting line-up and his side needed Ali Koiki to be alert in the opening two minutes when he got back well to deny Offrande Zanzala a one-on-one opportunity.
Northampton’s first big chance arrived on eight minutes when Louis Appere slipped in Eppiah but the angle was narrow and Cameron Dawson made himself big to keep the game scoreless.
Despite that opening though, Exeter were the better team for most of the first-half and they were causing real problems down their right side in particular with Aaron McGowan having to make a vital interception and then Matt Jay shooting straight at Liam Roberts.
McGowan injured himself in the process and tried to battle on but eventually had to make way for Joseph Mills who slotted in at centre-back as Town moved to a defensive threesome.
The blow of losing a key defender was softened just 60 seconds later when that man Pinnock fired Cobblers into the lead with a brilliant solo goal.
He received possession on the right, cleverly beat his man and then thundered a volley into the far bottom corner.
That was enough for the home side to take a lead into half-time despite Exeter continuing to impress, and Liam Roberts came to the rescue two minutes into the second-half with a brilliant close-range save from Timothee Dieng.
Eppiah nearly got through for a one-on-one chance at the other end he really should have doubled Town’s lead on the hour-mark after brilliant work from Appere but he shot into the body of Dawson.
Cobblers also had the ball in the net but Pinnock was correctly ruled offside in the build-up and 30 seconds later the ball was in the back of their net. Exeter took the free-kick quickly, broke up field and Nombe flicked home with his first touch of the game.
The hosts had to go for the win to keep control of their own destiny and they had several close shaves but the ball just wouldn’t go in, with Fraser Horsfall’s stoppage-time header hacked off the line.
Cobblers: Roberts, McGowan (Mills 28), Horsfall ©, Guthrie, Koiki, McWilliams, Sowerby, Pinnock, Eppiah, Hoskins, Appere.
Subs not used: Maxted, Dyche, Pollock, Kanu, Zimba, Rose
Exeter: Dawson, Sweeney, Key, Sparkes (Caprice 55), Grounds, Diabate, Dieng, Collins, Zanzala (Nombe 69), Jay © (Coley 55), Brown
Subs not used: Kite, Brown, Pond, Amond
Referee: Simon Mather
Exeter fans: 1,449