Goals from James Brophy and David Mooney in the second-half were not enough to see the O’s secure a winner as a Richard Peniket was the decider in the 79th minute.
Head Coach Justin Edinburgh made two changes to the side that were defeated by a single goal at Dover on the weekend.
Injury time winner David Mooney came in to the side as did James Brophy who started on the bench last weekend due to illness; in place of Alex Lawless who is out through injury while Craig Clay is out due to illness.
Gateshead got the game underway at the International stadium and took the lead within two minutes of play when Danny Johnson got across his man and swept the ball in to the back of the net.
The O’s looked for an almost immediate response when Lamar Reynolds got the better of his man inside the box but could only strike in to the hands of James Montgomery.
Jake Caprice was alert to block Scott Barrow’s shot on to the post at the far post after a cross from the right rolled across the box without any contact.
End-to-end action saw Reynolds’ corner met by defender Dan Happe at the back post but the effort rolled just wide of the target.
Gateshead were awarded with a penalty in the 16th minute when Johnson went down under a challenge from Happe. The Heed forward then sent Brill the wrong way to double the hosts lead.
Despite being two goals down, Reynolds continued to cause the opposition defence trouble when he got the better of his man and picked out Brophy at the back post, but somehow the wingers touch fell the wrong side of the post and out for a goal-kick.
Richard Peniket ended Gateshead’s long spell of possession with a good effort that required a smart save from the feet of Brill. The attempt that followed was cleared off the line by Josh Coulson.
On the stroke of half-time, David Mooney’s goal-bound header was somehow excellently tipped wide by Montgomery to keep the score at 2-0 to the hosts at the break.
James Brophy pulled one back for the O’s after 53 minutes when Reynolds’ initial cross was cleared only to the Orient wide man who finished with a lovely half-volley in to the back of the Gateshead net.
Minutes later, Gateshead saw Johnson cut on to his left foot and curl an effort over the target before Josh Coulson was inches away from connecting with Koroma’s cross at the far post.
After 70 minutes of play, O’s skipper David Mooney was free inside the six-yard box to head back across goal and in to the net from Josh Koroma’s excellent free-kick to bring Orient level on 70 minutes.
The action wasn’t finished there however, Barrow won the ball back out wide and crossed for Peniket who tapped the ball in to the back of the net to put the hosts back in the lead.
Gateshead held on to their lead in the dying moments to secure a place in the FA Trophy Semi-Finals.
GATESHEAD: Montgomery, Barrow, Kerr, Byrne (C), Fyfield, York (Vassell 87), Peniket, Johnson, Preston (Burrow 72), McLaughlin, Penn
SUBS: Hanford, McNall, Greenwood
BOOKED: Barrow (66), York (82)
GOALS: Johnson (2 & 16), Peniket (79)
ORIENT: Brill, Caprice, Coulson, Happe (Sotiriou 89), Widdowson, Adams, Reynolds (Harrold 82), Koroma, Brophy, Mooney (C), Bonne
SUBS: Grainger, Clayden
BOOKED: Mooney (90+3), Widdowson (90+4)
GOALS: Brophy (53), Mooney (70)
ATTENDANCE: 685 (125)
REFEREE: Peter Wright