Northampton twice came from behind to snatch a point at Sixfields.
The visitors shocked their high-flying opponents by taking a sixth minute lead.
Matt Lockwood latched on to Lee Steele's pass and his cross evaded the Northampton defence allowing Wayne Carlisle to slide in at the far post and knock the ball past Lee Harper.
Orient had the better of the chances in the first half and Michael Simpson drilled a shot just over the bar on 21 minutes.
But five minutes later the home side should have equalised.
Eric Sabin was clean through following Ashley Westwood's free-kick but with just Glen Morris to beat his lob was superbly cleared by Gaby Zakauni.
On the half hour, referee Olivier waved away strong appeals for a penalty when Marc Richards appeared to have been barged in the back, while five minutes later a Scott McGleish header dropped the wrong side of the post following Mark Hughes' free-kick.
Nine minutes from the interval Northampton got back on level terms following a flowing move. Josh Low found McGleish on the right and when the cross came in, Richards out jumped Morris to head the ball into an empty net.
Orient regained the lead after 62 minutes with Carlisle again the scorer. Andy Scott hit a cross from the left and the ex-Bristol Rovers midfielder thumped the ball into the back of the net from 12 yards.
Within three minutes Northampton had equalised for a second time after a error from Zakauni. The central defender under-hit his back pass and McGleish ran on to round Morris before slotting home from six yards.
On 75 minutes Carlisle should have completed his hat-trick but he blazed over with just Harper to beat, while three minutes from time substitute Jabo Ibehre's header appeared to be heading for the corner of the net before Harper produced a great one handed save to deny him.