Fans threw flares and ripped up parts of the Mohammed V stadium after Raja's 2-1 victory over Chabab Rif Al Hoceima.
The country's DGSN security service said in a statement that 31 people were arrested for "acts of vandalism".
FMRFF has banned fans from the next five Raja home matches and fined the club 100,000 dirhams (£7,170).
Footage on Moroccan media showed the fans, dressed in the club's green  colours, charging at each other. It was unclear how the clashes had erupted.
DGSN revealed 10 people had been arrested prior to the game.
Prosecutors have opened an inquiry into the fan trouble.
Two people were killed in fighting among fans of Raja de Casablanca on Saturday, the Moroccan Football Federation (FMRFF) has confirmed.