Danny Rowe curled home a fine free-kick on the hour mark for the only goal in an entertaining contest played in a good spirit.
Victory for the Coasters helped make up for defeat to Salford City on the same ground eight days earlier in the National League play-off final.
Fylde had far the better of the first half and really should have led at the interval after spurning some good chances.
In the second half Orient came far more into the game and struck the woodwork three times - twice before Rowe's goal and once as they chased an equaliser.
Rowe's big moment came when Fylde won a free-kick five yards outside the box, the striker curling it right-footed over the wall and into the roof of the net.
It delighted Fylde's travelling fans who numbered many more than at the play-off final.
This was the second game of the afternoon under the Wembley arch, Chertsey Town having beaten Cray Valley 3-1 after extra-time in the FA Vase, the combined attendance for the games being 42,962.
Fylde lost the services of Neill Byrne early in the contest, the skipper clashing heads with Orient's Josh Coulson as they challenged for a cross.
Byrne was down on the turf for a couple of minutes before being able to walk off unaided and the defender seemed keen to play on.
But after a discussion on the touchline, Byrne conceded defeat in his attempt to go back on and was replaced by Tom Brevitt.
The Coasters went on to have the better of the first half and certainly had the better chances.
An early involvement for substitute Brevitt saw his cross from the right channel pick-out Andy Bond in the middle but the midfielder could only steer a shot wide as the ball bounced up to him off the turf.
Soon after that, Nick Haughton's fine pass played Rowe in behind the Orient defence, his low angled shot pushed away by goalkeeper Dean Brill.
When the ball was recycled on the left hand side of the box, Haughton fired a shot into the side-netting.
Alex Reid's first-time shot on the half-turn from 20 yards was parried behind by Brill as Fylde maintained their pressure
A first decent chance for Orient fell in the 25th minute, James Brophy's low shot saved at the foot of the post by Jay Lynch.
Josh Koroma fired two chances over the bar within a couple of minutes of one another as the East London outfit enjoyed a brief purple patch.
Two good chances fell Fylde's way in the run-up to the interval and really they should have led going into half-time.
In the 43rd minute Rowe's ball across the box found Bond beyond the far post but from close range lifted his shot too high.
Two minutes later, Haughton's pass played in Alex Reid in front of goal but with just Brill to beat took a touch before stabbing a left-foot shot straight at the keeper.
With the second half less than a minute old, Brill dived low to gather a cross at Reid's feet.
There was a let-off for Fylde in the 50th minute when Orient were the width of the woodwork from going in front.
Haughton's foul on Jobi McAnuff gave away a free-kick 25 yards out, one which substitute Jordan Maguire-Drew curled left-footed over the wall and against the post.
The ball was put out for a corner and when that was delivered into the middle, Daniel Happe was first to it but headed over the bar.
Fylde's response saw Ryan Croasdale's pass play in Reid down the right hand side of the box, his shot finding the side-netting.
The woodwork came to their rescue a second time in the 57th minute as Maguire-Drew's corner from the right was won in the air by Marvin Ekpiteta, his header coming back off the post.
After riding out the pressure, Fylde took the lead as the clock hit the hour mark.
Reid was fouled by Coulson five yards outside the box, to the left of goal.
Once Orient had lined-up their wall, Rowe whipped the free-kick right-footed over it and into the net, Brill rooted to the spot.
For a third time hit the workwork in the 70th minute, Joe Widdowson given the room to cut in from the left and hit a low shot against the post.
The rebound fell to Maguire-Drew, his shot on the way into the net until it struck his team-mate Matt Harrold who had just come on as a substitute.
Maguire-Drew met a McAnuff cross and volleyed just wide as Orient upped the pressure in search of parity.
In the closing stages, Harrold sent a header down into the tuf and up over the bar after meeting a Maguire-Drew cross from the left.
Croasdale wasn't far away from adding to Fylde's lead at the other end in the 88th minute, his low shot after a neat exchange of passes involving Zaine Francis-Angol and Rowe, going across goal and wide of the far post.
AFC Fylde: Lynch, Birch (Crawford 90), Tunnicliffe, Byrne (Brewitt 12), Francis-Angol, Croasdale, Bond, Philliskirk, Reid, Haughton (Odusina 74), Rowe. Subs (not used): Hardy, Griffiths.
Leyton Orient: Brill, Ekpiteta, Coulson, Happe (Harrold 68), Turley (Maguire-Drew 46), Clay, Brophy, McAnuff (Lee 78), Widdowson, Koroma, Bonne. Subs (not used): Ling, Sargeant.
Referee: Andy Madley (West Yorkshire)
Attendance: 42,962 (combined FA Trophy and FA Vase attendances)