The visitors had taken an early lead, as Rob Hunt claimed his first goal for the club, but the Cobblers hit back with a quickfire double early in the second half before Kieron Bowie saw red.
And Richie Wellens saw his side claim a share of the spoils in the sixth extra minute.
Ed Turns and Aaron Drinan came into the starting line-up for O’s as Joe Pigott and Theo Archibald were named among the substitutes.
And O’s came under early pressure, as the Cobblers forced a couple of corners and Turns made a brave block with his head after a slip.
Dan Happe was booked on 10 minutes from a foul on Sam Hoskins, with Marc Leonard forcing a save from Sol Brynn at his near post.
But O’s took the lead on 14 minutes when the ball fell to Hunt on the right side of the box and his angled effort found the bottom corner of the net.
Brandon Cooper was shown a yellow card for a foul on Hoskins soon after, while Jordan Graham picked out Idris El Mizouni but his effort was claimed by Lee Burge.
El Mizouni saw another effort spilt by Burge on 21 minutes, but the hosts cleared the loose ball as Drinan looked to pounce.
Hoskins then angled an effort from a low cross over at the other end, as Northampton looked to respond, and Hunt conceded a corner as Bowie looked to convert at the far post on 33 minutes.
But Brynn remained largely untroubled in the visiting goal, even though O’s were seeing little of the ball towards the end of the first half.
Drinan did superbly well to win possession and play in El Mizouni four minutes before the break, but Burge was equal to his effort from the edge of the box.
And O’s then produced a fine move that saw Galbraith pick out Drinan, who touched the ball off for Graham to fire just wide.
Northampton levelled just four minutes into the second half after breaking upfield from an O’s corner, with Hoskins seeing his effort deflect over Brynn.
And they were awarded a penalty on 51 minutes, with Hoskins converting from the spot to complete a quick turnaround.
Cooper headed over from a corner as O’s looked to hit back, before the home side were reduced to 10 men on 58 minutes as Bowie was shown a straight red card.
And Cooper fired over when Hunt’s shot fell his way on 64 minutes, as O’s tried to make their extra man count.
Hunt made way for Archibald in the first change of the night for the visitors, with Pigott replacing El Mizouni moments later, and Ruel Sotiriou headed wide from Graham’s cross.
Brynn produced a vital save to deny Leonard a third Northampton goal on 69 minutes, with O’s countering to win a corner. But Pigott saw an effort ruled out for handball.
And Wellens made a double switch with 17 minutes to play as Forde and Tom James relieved Drinan and Happe, with Sotiriou forcing a fine save from Burge before Archibald fired wide.
Burge was booked for time wasting over a goal kick, but made a double save to deny Sotiriou and Jordan Brown on 87 minutes after Pigott had fired wide.
And James and Graham fired high and wide of the target at the start of injury time, before Forde squeezed home in the 96th minute after Graham had kept his footing and fired into the danger zone.
Leyton Orient: Brynn, Cooper, Happe (James 73), Turns, Hunt (Archibald 65), Galbraith, Brown, El Mizouni (Piggott 66), Graham, Drinan (Forde 73), Sotiriou. Unused subs: Sweeney, Howes, Moncur.
Attendance: 6,193 (including 716 O’s fans).
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