It was the visitors that came closest to scoring inside the first minute, but after the ball broke for Sean Clohessy, the right-back could only fire over the crossbar.
However, Hartlepool were on terms eight minutes later - Kudus Oyenuga converting from the penalty spot after a handball inside the box.
Oyenuga again came close for the hosts just before the 30-minute mark, but this time, his effort was over the Orient crossbar as the sides remained on terms approaching the half-time interval.
The hosts scored the game's all-important third goal in the 70th minute, however, when on-loan Crystal Palace midfielder Jake Gray's deflected strike from outside the box found the back of the net.
Gray was not finished, however, and added his second of the match five minutes from time to secure all the points for the home team.
The result has moved Hartlepool into 19th position in the League Two table, while Orient remain in seventh.