High-flying Posh had already cleared off the goal-line from Orient strikers Simon Church and Scott McGleish when they raced into a 2-0 lead.
Chris Whelpdale met a cross from Paul Coutts to head them in front and Aaron Mclean set up midfielder Sergio Torres to fire in a shot that eluded the grasp of Orient goalkeeper Jamie Jones.
McGleish reduced the arrears from the penalty spot after Charlie Lee had handled, only for captain Russ Martin to restore Peterborough's two-goal lead when he headed home Coutt's cross in first-half added time.
Orient replied through McGleish following a Jason Demetriou free-kick.
The home side matched their opponents in most areas and had more possession during the closing stages of an entertaining, windswept game, but it was not enough to save them from their ninth home defeat of the season.