Two goals from striker Eifion Williams gave new Harlepool boss Mike Newell a winning start.
Newell, appointed on Thursday, saw Williams strike once in each half as table toppers Hartlepool piled on the misery for struggling Orient as they recorded their sixth away win.
However it was rough justice on the hard working home side and Orient manager Paul Brush was furious that referee Clive Wilkes allowed Harlepool's winner after there appeared to be a foul on Chris Tate in the build up.
Brush said: "They were two poor goals to conceed but I didn't feel that we had the rub of the green with a couple of the decisions. I'm choked we didn't come out of the game with anything - except a bit of credit." While Harlepool boss Newell said "I'm delighted with the result, I'm glad to get this one out of the way it was a difficult place to come for my first game and there was a bit of pressure on the players.
But they responded well and the two goals from Williams were excellent ".
It was Orient who started well and Tate, making his first appearence for a year, forced Hartlepool keeper Antony Williams into a save after 22 seconds.
Indeed , John Martin had twice gone close for Orient before Harlepool took the lead on 25 minutes when Ezomo Iriekpen's poor clearance caught Williams who raced through and slotted the ball over Scott Barrett.
Gary Fletcher should have levelled with a close range header two minutes later before Hartlepool almost stretched their advantage on the stroke of half time.
Martin headed Darrell Clarke's effort off the line and then Paul Smith smashed a shot against the bar.
Orient were level on 69 minutes when substitute Scott Canham headed home just 3 minutes after coming on following a Matthew Lockwood cross. But a minute later Williams slid the ball home after an excellent pass by Richie Humphreys despite Orient's protests