Orient dominated the first half and were full value for their half time lead.
But Hartlepool came back with an improved display in the second period after a half-time roasting from manager Danny Wilson, and they went close to winning it.
Orient made four changes after their Boxing Day hammering at Bournemouth and they made a big difference with a much improved team display.
Hartlepool, meanwhile, lost Willie Boland and James Brown to flue, and one or two other players were feeling the affects of a bug sweeping through the club.
Adam Chambers capped his great individual performance with Orient's goal on 33 minutes, sent through by former Hartlepool star Adam Boyd before rolling his shot under the body of keeper of Jan Budtz.
The home team were level ten minutes after half-time when Orient failed to cope with a cross from Robbie Elliott and when they could only clear to the edge of the area, Ian Moore slammed a low shot into the bottom corner through a forest of legs for his ninth of the season.
Hartlepool sub Michael Mackay blasted a great shot on the turn against the Orient bar on 66 minutes, his first touch a minute after going on.
That was as close as either team could go and although Hartlepool had more of the game in the last quarter, they couldn't create any real chances once Mackay's effort missed and Michael Nelson blasted the rebound over the bar.