Town trailed at half-time after Rob Hunt’s early opener but the game flipped in the space of three second half minutes as Sam Hoskins scored his seventh and eighth goals of the season to enter the top-10 in the all-time list of Cobblers goalscorers.
However, the mood dampened around Sixfields when Bowie was shown red only six minutes later and from then on Town relied on desperate, frantic defending to keep Orient at bay, and it looked like they had done enough as five of the eight added minutes passed.
It was not to be though and Shaq Forde broke home hearts by snatching an equaliser, although Cobblers should still reflect on this as a decent point after putting in such an immense shift with 10 men.
Jon Brady made a tactical switch for the visit of Orient as he went to three at the back and handed a full Cobblers debut to Jordan Willis, who replaced Tyreece Simpson in the only change from Saturday.
Cobblers bossed the first five or six minutes and launched multiple attacks down both sides but Orient weathered the storm before they hit the front with their first shot on 14 minutes.
A patient period of possession for the visitors ended with Hunt receiving possession on the right corner of the penalty box and he caught out Lee Burge with a shot inside his near post, the goalkeeper unable to keep the ball out despite getting a decent hand to it.
Town had some good moments but they weren’t creating anything meaningful and it could have got worse 20 minutes in when a long throw found Idris El-Mizouni in the middle of the box and he was denied by Burge.
A Sam Hoskins flick from Marc Leonard’s cross flew over and numerous corners came and went but although the home side played some good football and enjoyed plenty of control, Orient’s attacking play had more cutting edge as Aaron Drinan shot straight at Burge and Jordan Graham fired wide.
The deficit remained at one at half-time but everything changed in a dramatic three-minute period at the start of the second half.
Cobblers were back on level terms thanks in part to great work by Shaun McWilliams who won the ball back and released Hoskins and Town’s main man did the rest, driving into the box and finding the far corner via a deflection.
And three minutes later the hosts were ahead.
Akin Odimayo was brought down in the penalty box and Hoskins had no hesitation in stepping up after his miss at Shrewsbury as he placed his spot-kick beyond the reach of Sol Brynn.
But Northampton’s jubilation was cut short when they lost a man just shy of the hour-mark.
It appeared an innocuous incident but the linesman spotted something off the ball and Bowie was given his marching orders.
It was all one-way traffic from there as Brandon Cooper blazed over before Sotiriou really should have levelled things up but somehow he nodded wide from virtually underneath the crossbar.
Brynn saved smartly from Marc Leonard as Town broke away but the vast majority of the action was happening at the other end where Orient saw a goal disallowed before Burge tipped over Sotiriou’s volley.
It was all hands on deck at the back and Burge’s services were needed again with a double save before Graham curled just wide in the first of eight added minutes.
Just as it looked like they would hang on, Cobblers were denied in the 96th minute when the dangerous Graham inevitably created Orient’s equaliser, his cross turned in by Forde for a share of the spoils.
Cobblers: Burge, Willis (Lintott 79), Sherring, Monthé, Odimayo (Hondermarck 73), Brough (Koiki 79), McWilliams, Leonard, Pinnock, Hoskins (Simpson 84), Bowie
Subs not used: Thompson, McGowan, Haynes, McGowan
Orient: Brynn, Turns, Happe (James 73), Brown, Cooper, Hunt (Archibald 64), El-Mizouni © (Pigott 66), Drinan (Forde 73), Galbraith, Graham, Sortiriou
Subs not used: Sweeney, Howes, Moncur
Referee: Jacob Miles
Orient fans: 716