Gary Alexander grabbed a last minute equaliser to give Orient a point and help extend Martin Ling's spell in charge as caretaker manager.
Ling replaced Paul Brush a month and club chairman Barry Hearn was due to appoint a new manager on Monday.
But he revealed after the game: "I've decided to give Martin the job until Christmas.
"It's been a tough call because we had some very good applicants but Martin has taken 11 points from six games - and that's with several senior players out injured.
"So he deserves a chance, but we will need to be close to the play-offs by Christmas, certainly on the first page of Ceefax," smiled Hearn.
"We were second from bottom when he took over so at least we are making some progress," concluded the Chairman.
In a tense encounter Orient were never at their best and Northampton looked to be on their way to their first victory under new manager Colin Calderwood.
Former O's player Josh Low, who spent an unhappy time at Brisbane Road, looked to have scuppered Ling's chances when he steered the ball home following Martin Smith's powerful run down the right on 59 minutes.
Orient huffed and puffed for a leveller and Alan McCormack saw a shot saved by Town keeper Lee Harper and when skipper Dave McGhee fired wide Orient's hopes looked over.
But a minute from time David Hunt's free kick bobbled around the visitors' penalty area before Alexander smacked home his third goal in five games.
In a dramatic ending McCormack was sent off for the second time this season after a bust up with Chris Hargreaves but Orient almost grabbed an injury time winner when Dean Hammond headed straight at Harper.
Ling admitted: "I'm quietly pleased to have been given the job until Christmas - I think the Chairman looked beyond this performance and ten games gives me a chance to prove myself again and I am happy to take up the challenge."