Leading from Andy Kirk's superb opener, Northampton failed to capitalise on their early advantage and Orient dominated for long periods before finally drawing level in the second half.
Both sides had chances to win it late on but both seemed content to settle for a point.
Scott McGleish had an early chance for Northampton, shooting straight at Glyn Garner after Jason Crowe had created the opening.
But Orient went close twice in as many minutes at the other end, Joe Keith firing just over and Paul Connor finding the side netting after the Northampton defence was caught out by a pass from Gaby Zakauni.
Kirk shot Northampton into an eighth minute lead, picking up the ball in his own area before advancing to unleash a 25 yarder into the top corner.
Orient came strong as the half wore on with Michael Simpson shooting just wide and Craig Easton having an effort tipped over by keeper Lee Harper.
Orient continued to have the greater possession in the second half with Northampton looking dangerous on the counter attack.
Harper prevented Mackie from equalising before the Orient defender finally did so in the 65th minute, heading home a corner from Matthew Lockwood.
Lockwood continued to be a threat on the left flank with his dangerous crosses and Orient had chances with Connor shooting just wide, substitute Gary Alexander heading over and Lockwood himself just off target late on.
But Kirk missed the best chance of the second half, heading straight at keeper Garner in the 75th minute after McGleish had done well to get in his cross.
McGleish, who had seen an earlier effort ruled out for his offside before the Orient equaliser, also went close on two occasions.
Firstly he headed over a cross from Gavin Johnson and late on shot just wide with a first-time effort.