Boyd's 25-yard strike, nine minutes from time, ended Hartlepool's run of four straight league victories.
On a bleak afternoon the visitors started well and with the wind in their favour created two chances in the first seven minutes.
But Hartlepool striker Joel Porter was first denied by home goalkeeper Glenn Morris and then sent his second shot over the bar.
On-loan striker Kevin Kyle then headed wide for the visitors, who created the better openings early on.
But gradually Orient started to take control with some slick soccer and after Dean Morgan shot wide when well-placed, the home side rattled the woodwork twice in three minutes.
First Sean Thornton saw his free-kick from 25 yards thud against the bar with keeper Arran Lee-Barrett well beaten.
Then Orient winger JJ Melligan went on a wriggling run before cutting in and firing a shot that came crashing back off the bar.
After the interval the game became a little more scrappy as Orient dominated without creating too many clear-cut openings.
The lively Melligan shot over on 54 minutes and then Morgan set up Danny Granville with a great ball, but the defender's effort was deflected wide.
Adam Chambers then fired over from 20 yards after another good run by Melligan as Orient continued to huff and puff.
The breakthrough finally came on 81 minutes. Boyd, the former Hartlepool hitman, had replaced Sam Parkin just five minutes earlier, and he delivered the killer blow.
Chambers looked to have run into trouble, but the ball fell kindly for Boyd who cracked it home from outside the box and watched it take a deflection off a defender to wrongfoot Lee-Barrett.