AFC Fylde defender Arlen Birch was shoved by a pitch invader shortly after the late goal that sent the Coasters to Wembley.
The players were celebrating Alex Reid's last gasp winner against Stockport County yesterday, which booked Fylde a place in the FA Trophy final, with two people from the crowd running on the Edgeley Park turf to confront them.
A video taken from the stand showed one shoving Birch, 22, with a brief melee ensuing. A steward then stepped in, with both supporters then ejected from the stadium, a club insider said.
The Football Association (FA) is understood to have launched an investigation into incident, which came just weeks after Aston Villa's Jack Grealish was assaulted on the pitch by a supporter of rival club Birmingham City.
The same day, an Arsenal fan ran on the pitch at the Emirates to shove Man Utd's Chris Smalling.
Fylde manager Dave Challinor said: “You have one idiot who runs on at Birmingham and all of a sudden now everyone thinks it’s clever to do it.
“It’s wrong, it really is. What you can’t do is say that’s synonymous of all their fans, it’s not, it’s just some idiot running on the pitch."