Everton have been fined £300,000 over the two pitch invasions during their Premier League win over Crystal Palace at Goodison Park on 19 May.
The hosts fought back from 2-0 down to secure their Premier League survival in the penultimate game of the season.
Fans came onto the pitch to celebrate Dominic Calvert-Lewin's 85th-minute winner and after the final whistle.
The Football Association said fans used "threatening and violent behaviour" as they invaded the pitch.
Everton admitted failing to control the crowd.
