Defender Dan Happe had given the O’s the lead at the break, though Stevenage levelled 10 minutes after the restart with a header.
The O’s were able to edge in front in the final 15 minutes however, with substitute Sam Dalby getting in behind the hosts defence to apply a calm finish before Romauld Boco pounced on a goalkeeping error to settle the tie.
With a number of players in search of minutes, Orient included summer additions Jamie Sendles-White and Romuald Boco in the starting XI, along with a number of younger professionals and two trialists on either wing.
From kick-off it was the hosts who went in search of an immediate breakthrough, as a ball out to the right saw Andronicos Georgiou find some space before being having his shot held by Sam Sargeant in the O’s goal.
Following a brief spell of dominance from the hosts, Orient soon grew into the game and managed to break the deadlock with 19 minutes played as defender Dan Happe was on hand to convert from a Boco corner.
Georgiou appeared to be the liveliest threat for Stevenage and the winger created an opportunity to level the score soon after, but despite racing clear of the defence and lifting the ball over the rushing Sargeant his shot dropped wide of the post.
With the interval approaching Orient then created two chances in quick succession, as first Josh Koroma controlled well in the area and poked an effort wide, before Boco saw a low shot smartly parried behind by the Boro ‘keeper.
Following the restart both sides were then denied by the frame of the goal within a minute of each other, as the crossbar first denied the hosts, and then Orient as Trialist B saw his drilled shot crash back off the underside of the woodwork.
The tie was soon level as a Stevenage trialist found space on the 55th minute to head home from a Ben Wilmot cross.
Both sides were limiting each other to minimum chances as they battled well for dominance, and with the 75th minute approaching Koroma worked a chance brilliantly in the area but could only fire wide of the far post after cutting inside the area.
Substitute Sam Dalby was able to restore the O’s lead two minutes later however, as the young forward showed a good turn of pace to get in behind the Boro defence and kept his composure to smartly flick the ball with the outside of his boot beyond the reach of the goalkeeper.
Two soon became three for Orient as Sam Alderson’s cross was spilled by the ‘keeper, and Boco was on hand to take a touch before stroking the ball into an empty net.
ORIENT: Sargeant, Judd, Sendles-White (C), Clark (Pollock 76), Happe, Barker (Haxhiu 76), Moncur (McLean 64), Trialist A (Dalby 61), Trialist B (Alderson 72), Boco, Koroma (Sotiriou 76)
GOALS: Happe (19), Dalby (77), Boco (81)