Following a goalless first half Billy Paynter fired Hartlepool ahead four minutes into the second half with a close range finish, before Nathan Thomas sealed a Pools victory with an individual strike on the 69th minute.
On the back of the 1-0 defeat at Accrington Stanley, player-manager Kevin Nolan made two changes for the visit of Hartlepool.
Jack Payne and Ollie Palmer came into the side, as defender Shaun Brisley missed out through injury while Sammy Moore dropped to the bench.
Brisley’s absence meant a reshuffle in defence, as captain Sean Clohessy dropped back to right back and Nicky Hunt moved across to partner Peter Ramage at centre half.
There was also a notable inclusion on the bench as first year scholar and forward Josh Koroma was named in the squad for the first time.
Heavy rain throughout the night had seen AFC Wimbledon’s lunchtime kick-off against Portsmouth postponed, but there were no such concerns at the Matchroom Stadium as the O’s lined up in a 4-3-3 formation which saw top scorer Jay Simpson play just behind Ollie Palmer and Armand Gnanduillet.
It was two of Orient’s strikeforce who nearly broke the deadlock five minutes in, when Palmer intercepted a loose pass 20 yards from the Hartlepool goal before Gnanduillet poked his through ball over the bar.
Hartlepool arrived in E10 unbeaten in their previous five matches, and it was the visitors who came close two minutes later when defender Adam Jackson headed Nathan Thomas’ cross wide at the far post.
Throughout the opening exchanges Orient were struggling to really get going but enjoyed a dominant five minutes midway through the first half which started with Gnanduillet heading Jerome Binnom-Williams’ cross over from six yards out.
A minute later Nicky Hunt lofted a terrific pass down the left to which Palmer brought down into his path and beat several defenders to cut into the box before seeing his shot deflected just wide of the pass despite beating Pools goalkeeper Trevor Carson.
Midfielder Nigel Atangana then suffered a similar outcome from the subsequent corner, seeing his low drive deflected wide from just inside the area before Kevin Nolan volleyed a tame effort at Carson from a Sean Clohessy cross.
Having failed to make the most of the brief pressure, the O’s then looked to be going into the break a goal down when Hartlepool captain Billy Paynter headed Carl Magnay’s free-kick beyond Alex Cisak, but the flag was correctly raised for offside as the sides went into the break goalless.
Following the interval both sides returned for the second half unchanged, and having been denied the opener just before half time Hartlepool opened the scoring four minutes after the restart when Paynter slid in at the far post to finish Jake Carroll’s low cross.
With just over an hour played the O’s then made a double change as Frazer Shaw and Blair Turgott came on for Gnanduillet and Nolan.
The substitutions saw Orient change to a 4-4-2 formation as Binnom-Williams moved forward to left midfield with Turgott on the other flank.
Despite the change in formation the hosts were then given it all to do on the 69th minute when Pools forward Nathan Thomas danced his way beyond Shaw on the edge of the box before powering a shot beyond Cisak to double the visitors lead.
Hartlepool midfielder Lewis Hawkins then took aim from distance five minutes later, but with his effort looking destined for the top corner Cisak produced a great dive to tip his effort round the post.
In response to the chance Orient made their final change as Lloyd James came on for Jack Payne in the centre of midfield, and moments after his introduction the O’s had two great chances to pull a goal back.
With the match approaching the final 10 minutes a James corner was powerfully met by Binnom-Williams who saw his header cleared off the line, and despite strong appeals for handball referee Frederick Graham awarded another corner.
From the ensuing corner Binnom-Williams was then denied for a second time in a minute as his header from another James corner was superbly pushed away from goal by Carson who was at full stretch.
Time was running out for Orient to find a way back into the game, and with two minutes of normal time remaining Simpson was denied his 24th of the season when he turned well on Palmer's knockdown only to see his shot parried away by Carson.
Michael Woods had a chance to make it three for the visitors in stoppage time when played in through on goal, but Cisak was on hand to deny the substitute in what was the final chance of the game.
The defeat leaves Orient two points off the Play-Off places with seven games remaining ahead of the trip to York City on Saturday.
ORIENT: Cisak, Clohessy (C), Hunt, Ramage, Binnom-Williams, Payne (James 75), Atangana, Nolan (Shaw 61), Simpson, Palmer, Gnanduillet (Turgott 61)
SUBS: Gregory, Pollock, Moore, Koroma
HARTLEPOOL: Carson, Magnay, Bates, Jackson, Carroll, Featherstone, Gray (Walker 83), Hawkins (Woods 76), Thomas, James (Bingham 87), Paynter (C)
SUBS: Bartlett, Oates, Richards, Jones
GOALS: Paynter (49), Thomas (69)
BOOKINGS: Featherstone (52)
REFEREE: Frederick Graham
ATTENDANCE: 5,543 (359)