The O's arrived at the Sixfields Stadium were on a high, having conceded only one goal in six matches after a stunning November, but it took them only 72 seconds to fall behind.
That goal arrived when a cross by Andy Todd was only partially cleared and Liam Davis fired a 25-yard left-footer which beat Glenn Morris inside his right-hand post.
That Northampton failed to capitalise on their first-half domination could be attributed to their current striking problems as their frontmen have now failed to hit the target in their last six matches.
But they came close to adding to their lead with a near-post header from Jason Crowe, a rising drive from Nicholas Bignall which flew over the bar and a left-footer from Giles Coke which suffered the same fate.
Nothing had been seen of Orient as an attacking unit but out of the blue they equalised three minutes before the break through their midfield player John Melligan.
There was a neat link-up down the left between Dean Morgan and Jason Demetriou and, when the latter delivered his cross, Melligan's first header was parried by Frank Fielding in the home goal but he had no chance in keeping out the second.
Orient began the second half in a much more purposeful vein and could have snatched the lead with snap-shots from Tamika Mkandawire and Adam Chambers, while Crowe had to make a last-ditch clearance to stop a Demetriou cross reaching the danger zone.
Northampton rallied with purpose in the final ten minutes when they had penalty appeals turned down and almost produced a rousing finale with a crisp strike by Kyle Walker producing an excellent diving save by Morris in the visitors goal.