It was a `game of two halves`, with the O`s having much the better of the opening period, apart from the very end of it, and Pools doing much better in the second.
In front of the live BT Sport cameras, Orient made a lively start, despite having lost their last two matches.
And they went in front after 19 minutes when Josh Koroma played a lovely through ball for David Mooney, whose effort produced a decent save from Scott Loach, only for Jobi McAnuff to pounce on the loose ball and fire the O`s deservedly ahead.
Six minutes later, Macauley Bonne almost made it 2-0 when his shot from a cute Alex Lawless pass beat Loach but bounced back off a post.
But then in first half injury-time, a Nicky Deverdics free-kick was only half cleared and the ball was lifted back into the box for Jonathan Franks top volley past Charlie Grainger in the O`s goal.
And then within 2 minutes of the start of the second half, the game was turned on its head when Pools took the lead.
Another Deverdics free-kick was headed home by Rhys Oates.
Six minutes later, it was the visitors` turn to curse their luck as a Ryan Donaldson shot which took a deflection, beat Grainger but came back off the woodwork.
Orient`s confidence drained as the half wore on, but then as stoppage time ticked in, they pinned the visitors back and 2 minutes into time added on, a great cross from Lawless was headed narrowly wide by Bonne.
And on 94 minutes came the O`s final chance but McAnuff`s corner was headed goalwards by Bonne but a defender`s head managed to flick it over the bar.
So it was the 200-plus Hartlepool fans in the 3,867 crowd who will enjoy their long journey back to the north-east.
Harrison was a happy man and said: "It was a really good three points for us, especially after going one behind.
"We have had a very good week, it's the most enjoyable week I have had since I came here and there will be some refreshments drunk on the way home!
"The plan certainly wasn't to go 1-0 down but we didn't panic and the goals came at a very good time to score.
"I would have preferred a winner in the last minute! But we held on well and defended superbly."
He added: "We spoke at half time and changed a few things. We had to be a bit more narrow and not go chasing things.
"It was a reward for our fantastic fans who came down in great numbers."