Chris Whelpdale, Sergio Torres and Russell Martin netted for the Posh in a lively first half but Orient pushed them all the way although Scott McGleish's double was not quite enough.
In a frenetic opening Orient almost scored after three minutes when Simon Church rolled an effort across the goal and then Jimmy Smith saw a shot blocked.
But on six minutes Peterborough made the breakthrough when Whelpdale headed home from close range following a cross from Paul Coutts.
As the Posh surged forward, Orient keeper Jamie Jones blocked a shot from George Boyd with his legs, before the visitors struck again on 12 minutes.
This time Torres was the marksman when he saw his shot go under Jones after former O's striker Aaron McLean's clever run dragged the Orient defence out of position.
Peterborough had a scare when keeper Joe Lewis crashed against the post as he tipped away Andrew Cave-Brown 's cross which had taken a deflection off defender Chris Westwood.
Six minutes before the break Orient pulled a goal back when Charlie Lee was harshly adjudged to have handled Church's cross and McGleish smashed home the spot-kick.
But any revival hopes were quickly dashed when Martin headed home Dean Keates's corner in first half stoppage time.
Orient hit back in the second half and cut the deficit on 56 minutes when Jason Demetriou's free kick was touched on by Church into the path of McGleish who fired home.
Then Orient almost grabbed a point in stoppage time when Sean Thornton's free kick hit keeper Lewis but substitute Wayne Gray failed to find a finish from three yards.