Matt Harrold’s second half penalty proved just about enough for the win, before Myles Judd’s second yellow and late dismissal.
Wrexham got the game underway at a significantly less packed Racecourse Ground in comparison to how it was for our National League encounter.
Orient were dealt and early blow when Marvin Ekpiteta was forced off through injury however youngster Jayden Sweeney was a ready replacement.
The first clear chance of the game fell to Wrexham’s Luke Summerfield who struck against the post from distance after short passing play found the midfielder in space.
Jordan Maguire-Drew had the first chance on goal for the O’s and his effort from just outside the box almost caught Christian Dibble out in the Wrexham net, but he was able to tip the ball to safety.
Moments later, Cole Stockton had a similar effort to his team-mate Summerfield, however the forwards effort was ushered wide of the target by Dean Brill.
Shortly before the break, George Elokobi was alert to head away James Jennings’ cross before skipper Lee threw his body at the ball to block the rebound which looked goal-bound from Luke Young.
Orient’s best chance came a second before the whistle, Maguire-Drew played James Alabi through on goal, the forward cut on to his left and shoot but was excellently denied by Dibble’s left hand.
Matt Harrold gave the O’s the lead shortly after the hour mark, he converted from the spot after James Brophy was brought down by Wrexham skipper Mark Carrington.
Myles Judd was shown a red card for his challenge on Rekeil Pyke after 78 minutes and Orient were forced to defend their lead.
Newly introduced Josh Koroma had two chances to stretch the lead, firstly Brophy found the forward in space but he hit the ball wide of Dibble’s net.
The second chance came when he raced through on goal himself, but dragged the shot away from the far post in what was a good chance.
Wrexham’s man advantage meant they had the majority of the ball in the dying moments and the final chance came from new man Ben Tollitt who won the ball back in midfield, advanced on goal but struck over as the referee called time on the FA Trophy tie.
WREXHAM: Dibble, Roberts, Jennings, Summerfield, Young, Oswell (Pyke60), Carrington (C) (Rutherford 81), Walker, Wright (Tollitt 77), Lawlor, Stockton
SUBS: Lainton, Holroyd
BOOKED: Young (62)
ORIENT: Brill, Judd, Ekpiteta (Sweeney 16), Happe, Elokobi, Maguire-Drew (Koroma 75), Lee, Lawless, Brophy (Gorman 83), Harrold, Alabi
SUBS: Sargeant, Sotiriou
BOOKED: Judd (32)
RED: Judd (78)
GOALS: Harrold (63)
REFEREE: Peter Gibbons
ATTENDANCE: 1,949 (105)