Adam Boyd came off the bench to score the winner against his former club.
The Orient striker had only been on the pitch for five minutes when he collected the ball from Adam Chambers and fired home from 25 yards.
Earlier, Hartlepool posed threats through Joel Porter and Kevin Kyle, and Orient's Tamika Mkandawire headed wide.
Orient midfielder Sean Thornton hit the bar with a free-kick and JJ Melligan cut in and shot against the Hartlepool post before Boyd found the net.
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Booked: Saah, Granville, Thornton.
Goals: Boyd 81.
Hartlepool: Lee-Barrett, Sweeney, Nelson, Collins, Humphreys (Robson 84), Brown, Jones (Liddle 61), Clark, Monkhouse, Porter (Foley 84), Kyle. Subs Not Used: Budtz, McCunnie.
Booked: Kyle, Monkhouse.
Att: 3,638
Ref: Gavin Ward (Surrey).
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