Peter Hartley, after 88 minutes, and Luke James, deep into stoppage time, gave Pools the most unlikely of victories to keep their hopes of survival intact.
A seventh-minute penalty from Martin Rowlands, awarded for a handball in the area by Neil Austin, appeared to separate the sides and the O's looked good for the win.
Rowlands' spot-kick was the sixth penalty Pools have conceded at home in eight games.
The O's kept Pools at a distance for most of the game, with central defender Scott Cuthbert producing a number of blocks when the home side were able to shoot.
The visitors were denied a second after 29 minutes when goalkeeper Scott Flinders backpedalled to push out a goalbound Shaun Batt header from a lovely Gary Sawyer cross.
As half-time approached, Cuthbert excelled to stop goalbound shots from James Poole and twice from Jon Franks.
Second-half openings were scarce for both sides.
But Evan Horwood swung over a corner for Hartley to power in with just two minutes remaining and then James, with 30 seconds of five minutes of added time to go, won it with a snap-shot from the edge of the area after the O's failed to clear.