Defeat at Victoria Park has left Orient four points above Wycombe, who dramatically lost 4-3 at home to Notts County, and a place above the drop zone with one game, at home against Rochdale to come.
Pools goalkeeper Scott Flinders made a stunning stop to deny Kevin Lisbie, five minutes before Pools took the lead when Andy Monkhouse headed down in the penalty area and Antony Sweeney lashed in his ninth goal of the season from close range.
But the visitors equalised in the 34th minute. Pools lost possession and Jamal Campbell-Ryce broke away to clip a deft finish across Flinders.
Flinders again saved well from Lisbie when the striker was clean through. But Pools went ahead when Ryan Noble glanced home Evan Horwood's deep cross from eight yards.
Orient had two strong penalty shouts rejected by referee Steve Rushton as they scrapped for a leveller, the first of which looked a cast-iron spot kick for a handball offence against Monkhouse.