The spectators entered the Melbourne Victory supporters' bay during the top of the table A-League match, starting multiple fights and throwing cans during the second half.
Phoenix general manager David Dome said the club has "zero tolerance for anti-social behaviour".
"These individuals are not welcome at Phoenix games and we will seek sanctions against them, including potentially banning them from the A-League if charges are proven," Dome said.
"This would be an unprecedented step for the club. There currently aren't any Phoenix fans who are on the league's banned list.
"We are working with the police to identify the culprits."
The club will also work with management Sky Stadium, who are responsible for venue security.
"I'd like to apologise to all of the Victory supporters...unfortunately the behaviour of a small number of people took away from what was a great occasion on Friday night.
The match ended in a one-all draw.
"It was unquestionably one of the most dramatic games of the season...so it is very disappointing to have a small group of idiots engage in behaviour that no one else in the crowd wanted.
Dome said Victory and Phoenix fans mixed freely after the game "so we know this was an isolated incident and not representative of our fans."