A second-half goal from Matt Harrold sparked the come-back before Dan Happe’s late header sent us through to the next round.
Orient got the game underway and the two sides were equal in the opening stages. Both Danny Lewis and Dean Brill had an early feel of the ball but it was only to gather the danger in their respective boxes.
The home side had a spell of possession which firstly saw James Armson run through on goal, one-on-one with Dean Brill who made an excellent save.
Then, Dale Gorman was adjudged to have fouled Lee Ndlovu just outside the area and a free-kick was awarded to Brackley.
Adam Walker stepped up and hit a powerful effort goal-wards but Brill was called into action again to deny the attempt.
Shortly before 20 minutes had gone, Orient saw Macauley Bonne fire over after McAnuff’s search for Dan Happe in the box fell to the forward at the penalty spot.
Brackley took the lead after 25 minutes when Lowe kept the ball in play on the left and sent a cross in for Ndlovu to tap home.
Brill had to stay alert to somehow block the bullet header from Brackley Town captain Gareth Dean who found space in the centre of the goal following a corner-kick.
Orient pushed for a goal before the break after falling behind and it almost came after 33 minutes were on the clock when Marvin Ekpiteta saw his close ranger effort cleared off the line following good work on the right from McAnuff and Bonne.
Justin Edinburgh was forced into an early second-half change after Ekpiteta was unable to continue following a clash of heads, he was replaced by Josh Coulson on 55 minutes.
Orient kept the pressure on the hosts and thought it paid off when the Maguire-Drew was brought down inside the area.
Bonne stepped up to take the kick up was denied by Lewis who dived the correct way to clear the danger.
Less than ten minutes later, newly introduced Matt Harrold popped up in the centre of the net to tape home from James Brophy’s low cross to draw us level on 74 minutes.
There was a shout for a second penalty when Clay seemed to be tripped after excellent one touch play on the left wing, however Richard Hulme waved play on.
Orient continued to apply pressure on the hosts and finally found the break-through to take the lead. Dan Happe got up highest at the back post to nod home from Maguire-Drew’s corner-kick.
The remaining eight minutes were wide open Brackley looked to send the tie to an equaliser but the O’s stood firm to progress to the Semi-Final of the FA Trophy .
ORIENT: Brill, Judd (Maguire-Drew 56), Ekpiteta (Coulson 55), Happe, Ling, McAnuff, Clay, Gorman (Harrold 65), Brophy, Bonne, Simpson
SUBS: Sargeant, Lee
BOOKED: Gorman, Clay (76)
GOALS: Harrold (75), Happe (83)
REFEREE: Richard Hulme