Following their FA Cup exit, Orient have put together a string of excellent results and followed up Saturday's outstanding victory at leaders Nottingham Forest with a narrow success at Northampton thanks to Connor's 79th minute winner.
Orient always looked good value for at least a point after restricting Northampton to few clear-cut chances and always posed a threat in the latter stages with the home side searching for the elusive winner.
Both sides enjoyed plenty of possession in the first half without posing too much of a threat in the final third.
For Northampton, Joe Burnell, Eoin Jess and Chris Doig all went close, while Matthew Lockwood, Luke Guttridge and Justin Miller went close for the visitors.
Orient keeper Glyn Garner kept his side on level terms in first-half stoppage time when he kept out a first-time effort from Jess following a knock down from Scott McGleish.
But Northampton keeper Mark Bunn produced the best save of the match early after the restart when he superbly tipped over a Wayne Corden free-kick.
Northampton stepped up the tempo in the second half and Garner was the busier of the two keepers.
He did well to get down to keep out a low drive from Ryan Gilligan and produced an even better save on the hour mark denying McGleish from close-range with a point-blank stop.
Lockwood almost put Orient in front with a 73rd minute free-kick which nearly caught out Bunn at his near post before the ball was scrambled away for a corner.
With Northampton stretched at the back, Orient caught them on the break and when Bunn failed to hold on to the ball on the edge of the area, Connor pounced to slip it into an empty net.
Northampton mounted some late pressure in a bid to salvage the point but the closest they came was deep into stoppage time when defender Sean Dyche headed over from a good position.