Josh Low marked his return from injury with a crucial winner as the Cobblers kept their play-off hopes alive.
Low had only been on the field for six minutes when he executed a brilliant left-foot chip which dipped over O's goalkeeper Glen Morris and into the top corner.
It was sweet for Colin Calderwood's men who had been reduced to ten men nine minutes earlier when Paul Reid was given his marching orders by referee Phil Joslin.
Low was adjudged to have been the last line of defence when his challenge left Wayne Purser on the ground and referee Joslin acted after being alerted by a flagging linesman.
Orient, who needed victory to keep their own play-off aspirations alive, carved out their share of chances.
But their afternoon was summed up by a brilliant injury-time overhead kick by substitute Chris Tate which struck the inside of a post before rebounding to safety.
Their manager Martin Ling said: "I don't like reading about teams who don't get what they deserve from matches, but anyone who saw this game would have come up with that conclusion.
"We have now lost the last two games against sides around us in the table and you would have to say the play-offs are looking remote." Orient also managed to cancel out a goal themselves. David Hunt's second-half header would have counted, but in following up and ensuring the ball went over the line, Purser's touch ensured the strike was cancelled out for offside.
Northampton hit the woodwork themselves, with Marc Richards letting fly a minute after the restart with a ferocious volley from the edge of the box which left Orient's crossbar shaking.
Cobblers' boss Calderwood said: "We had a little bit of luck and showed a lot of commitment and desire and managed to stay in the game.
"If you do that you are always more likely to score in front of your home crowd."