Josh Parker had headed the hosts into a 20th minute lead, and despite Orient looking the much better side after the break Tom Eaves fired a second 16 minutes from time.
James Dayton was able to pull one back four minutes later, but despite their best efforts Orient fell to a First Round defeat in which Joe Widdowson also picked up a second yellow card in stoppage time.
With loan duo Mark Ellis and James Brophy ineligible for the tie and defender Dan Happe ruled out with an ankle injury, Head Coach Steve Davis made three changes to the side that drew at Wrexham last weekend as Michael Clark, Joe Widdowson and Myles Judd came in.
The O’s also welcomed midfielder Alex Lawless back on the bench following a groin injury, though were without Jobi McAnuff who missed out due to a toe injury.
Following a slow opening few minutes at the Priestfield Stadium it was the hosts who grabbed a foothold of the tie, as forward Tom Eaves headed over from a Mark Byrne free-kick before Josh Parker fired straight at Charlie Grainger moments later.
O’s forward Macauley Bonne then defended well to block an Elliot List shot following a Gills free-kick, before Grainger was once again called into action on the 16th minute when he held an Eaves shot after the striker had been played in by Lee Martin.
The hosts were not to wait much longer for the opening goal however, as on the 20th minute they made the breakthrough when Parker burst into the box unmarked to head a List cross from the right beyond Grainger.
Having conceded the opener Orient looked to respond immediately when Club Captain David Mooney collected the ball inside the area before seeing his shot deflected behind by former O Gabby Zakuani for a corner.
With the 30-minute mark approaching List then held off Judd on the corner of the penalty area before firing wide, and moments later then latched onto a ball over the top before being brought down by Grainger just outside the box.
A free-kick was awarded to the Gills while Grainger was booked for the challenge, and from the set-piece Max Ehmer saw a powerful strike deflected off the wall and headed away.
Good work from James Dayton on the 38th minute then saw the midfielder wriggle beyond two Gillingham defenders and earn a free-kick. After seeing the free-kick cleared the midfielder then tracked back brilliantly to thwart a counter attack and slide in on List as he charged up a shot in the box.
Gillingham took their one-goal advantage into the break, and following the interval Orient made one change as Alex Lawless came on in place of Michael Clark.
The substitution saw Orient also change the formation, switching to a 4-4-2 diamond which saw Lawless sit at the base with Boco playing just off Mooney and Bonne in attack.
The change in system looked to have an immediate impact as Mooney fired over from a Dayton cross, in which proved to be the first of a number of O’s chances.
Bonne then turned well outside the area before drilling a shot wide on the 52nd minute, and soon after Dayton curled a 25-yard free-kick into the wall as the visitors upped the pressure before Boco fired a shot at Tomas Holy from distance.
With an hour played the O’s almost levelled in spectacular fashion, as Mooney brilliantly controlled the ball on his chest before firing a volley from 25-yards which was expertly pushed over by Holy.
From the set-piece Orient had another chance, this time Jamie Sendles-White connecting with a header which was pushed away by the ‘keeper.
Continuing to push Gillingham back, Zain Westbrooke was next to come close on the 65th minute as he controlled well on the edge of the area and drilled a shot goalwards which was tipped over the bar.
Orient then introduced Matt Harrold on the 69th minute, with the forward coming on in place of Boco in a move that saw Mooney drop into a slightly deeper role behind the front two.
Despite dominating the second half, the O’s were dealt a cruel blow on the 74th minute when Gillingham doubled their lead.
Eaves and Sendles-White both appeared to have a hand on each other before the forward threw the O’s man to the floor and drilled a low shot beyond Grainger.
The two-goal deficit was not to last long however, as Orient fired a 78th minute levelled as Dayton’s free-kick from the left managed to evade everyone and find the bottom corner for his first goal for the Club.
The two teams then came together on the 80th minute following a challenge just inside the Gillingham half, with Dayton and Judd being shown yellow cards for their involvement.
With time running out Jake Caprice then produced a brave piece of defending, throwing himself in front of a Parker volley to keep the score at 2-1 before five minutes stoppage time was shown.
The O’s were then forced to play the final three minutes of stoppage time with only 10-men, as Joe Widdowson was shown a yellow card after being adjudged to have pulled back Wilkinson as he looked to enter the penalty area.
It was a gutsy effort from the O’s in Kent, but there was to be no leveller at the Priestfield Stadium as Orient bowed out of the FA Cup.
GILLINGHAM: Holy, Clare, Ehmer, Zakuani, Ogilvie (O’Neill 79), Byrne, Hessenthaler, Martin (C), List (Wagstaff 57), Parker, Eaves (Wilkinson 75)
SUBS: Arnold, Mbo, Chapman, Cundle
GOALS: Parker (20), Eaves (74)
BOOKED: Clare (77), Wilkinson (80)
ORIENT: Grainger, Caprice, Clark (Lawless HT), Sendles-White, Widdowson, Judd, Westbrooke (Sotiriou 87), Boco (Harrold 69), Dayton, Mooney (C), Bonne
SUBS: Sargeant, Pollock, Clay, Dalby
GOALS: Dayton (78)
BOOKED: Grainger (35), Sendles-White (75), Judd (80), Dayton (80), Harrold (83), Widdowson (86)
SENT OFF: Widdowson (90+2)
REFEREE: John Brooks
ATTENDANCE: 3,659 (818 Orient supporters)