Gareth Evans had got Portsmouth off to a dream start with his fourth minute goal, though Jay Simpson levelled from the penalty spot after Adam Webster had been dismissed for a foul on Jobi McAnuff. With half time looming the O's then took the lead when Ollie Palmer headed the hosts ahead in stoppage time.
Five minutes after the break Orient were then also reduced to ten men when Mathieu Baudry was handed a straight red for reacting to a challenge from Michael Doyle, though from the ensuing O's free-kick Palmer claimed his second of the match with another fine header.
Evans then pulled a goal back for the visitors on the 66th minute with a calm finish, but despite a frantic final period Orient were able to claim all three points.
Ahead of the O’s final home game of 2015 Head Coach Ian Hendon made four changes to the side that started against Yeovil last Saturday.
Connor Essam returned in defence for his first start since the end of October, while Jobi McAnuff came back into the side following his wonderful 30-yard strike against the Glovers.
With Orient lining up in a flat 4-4-2 Sean Clohessy also came in to take up an unfamiliar position on the right of midfield and Ollie Palmer was selected to partner Jay Simpson in attack.
Despite the changes Orient looked second best from the start, and Portsmouth made the most of their early dominance when Gareth Evans put them ahead after deflecting Kyle Bennett’s cross in at the near post.
Jay Simpson then had a chance to equalise less than a minute later but the striker was unable to keep his shot down as he side-footed Sean Clohessy’s cross over the bar.
Bennett was proving a real handful during the opening ten minutes and played a huge part in their next attack only to be denied by Alex Cisak who then reacted superbly to push Caolan Lavery’s follow up header behind.
The match was then turned on its head on the 22nd minute however as Jobi McAnuff capitalised on a mistake by Adam Webster to earn a penalty which was the Pompey defender giving his marching orders.
Top scorer Simpson then stepped up confidently to stroke home his 17th of the season and level the tie.
Moments later McAnuff then came close to scoring a stunning goal for the second week in a row when he played a neat one-two with Simpson before unleashing a rasping strike which was pushed behind by Pompey’s Brian Murphy.
As the half wore on Ollie Palmer was growing increasingly into the game and the target man showed a neat bit of skill to turn away from his marker 20-yards out on the 37th minute before directing a left footed shot at Murphy.
The previous weekend had seen Orient concede in first half stoppage time but there was to be a complete contrast the hosts edged ahead just before the interval when Palmer managed to go one better and get on the end of Cole Kpekawa’s lofted ball into the box and flick a header into the far corner.
Palmer’s goal certainly made Ian Hendon’s team talk much easier after the break but five minutes into the second half both sides found themselves down to ten men as O’s skipper reacted badly to a challenge from Michael Doyle and was subsequently shown a straight red.
A free-kick had already been awarded for Orient before the incident however and two minutes later the hosts boasted a two-goal advantage when Clohessy’s lofted ball into the box was met by the dive of Palmer who excellently headed in his second of the match.
With both sides a man light the game was increasingly open and with an hour gone Cisak produced a wonderful save to claw away Evans’ header and prevent it from finding a way into the top corner.
Evans was not to be denied six minutes later however as Pompey broke quickly following an Orient attack and Bennett managed to slip in the midfielder who then reduced the deficit to one with a calm finish.
Certainly buoyed by the goal Pompey continued to throw bodies forward in search of a quick second but Cisak was in no mood to oblige as he first denied Ben Davies with a wonderful stop.
A minute later Cisak was then quick to punch a Davies cross away from the head of Lavery and Evans was then left with his head in his hands as he sliced the rebound over.
In a bid to cope with the pressure Frazer Shaw was then brought on in place of Simpson as the O’s reverted to a 4-4-1 for the final 17 minutes with Palmer leading from the front.
Having managed to contain the visitors John Marquis and Blair Turgott were then introduced during the final moments in place of Palmer and McAnuff, before seven minutes stoppage time was shown by the fourth official.
Two minutes into stoppage time Orient really should have wrapped up the win when Marquis intercepted a loose backpass to Murphy but the striker was denied first by the Pompey stopper as he tipped his shot onto the post before his follow up attempt was cleared off the line.
Cisak had been phenomenal between the sticks for the O's and in the sixth minute of stoppage time the Australian pulled off yet another fantastic stop to deny Matt Clarke as the hosts held on for the three points.
ORIENT: Cisak, Baudry (C), M’voto, Essam, Kpekawa, Clohessy, Pritchard, Payne, McAnuff (Turgott 88), Palmer (Marquis 82), Simpson (Shaw 73)
SUBS: Grainger, Dunne, Moncur, Kashket
GOALS: Simpson (23 pen), Palmer (45+1 & 52)
BOOKINGS: Essam (10), Palmer (53), Pritchard (89)
SENT OFF: Baudry (50)
PORTSMOUTH: Murphy, Davies, Webster, Clarke, Stevens, Evans, Hollands (Roberts 87), Doyle (C), Bennett (Chaplin 87), McNulty (Barton 24), Lavery
SUBS: Bass, McGurk, Tollitt, Close
GOALS: Evans (4 & 66)
BOOKINGS: Davies (32)
SENT OFF: Webster (24)
REFEREE: Graham Horwood
ATTENDANCE: 5,848 (1,316)