The collision knocked the ballboy to the ground.
Marrone was angrily challenged by Sydney FC substitute Matt Simon, who also ran in and shoved Marrone away from the ballboy.
Fox Sports commentator Simon Hill said Simon appeared to run in to get Marrone away from the ballboy. Simon's angry shove resulted in Adelaide United players running in from the field and the bench to protect their teammate.
That prompted Sydney FC players and officials to also enter the fray, sparking an AFL-styled melee which ran up and down the touchline and spilled over into the Allianz Stadium tunnel in front of the crowd of 13,452.
As the "free for all brawl" erupted, the ball boy initially remained stunned on the ground.
"Michael Marrone came over to get the ball from the ballboy," Peacock said in commentary for Fox Sports.
"The ballboy didn't give it. And (referee) Kris Griffiths-Jones knows the story and he's given a straight red. He is off. The poor ballboy is so rattled that it's not funny. He doesn't know what's going on.
"Michael Marrone tried to get the ball and ended up, it actually looked like a bear hug. The kid wasn't giving the ball up and it all escalated from there. It kicked off."
Hill described the melee as a "free-for-all".
The ballboy was spotted sitting with a police guardian after the fracas and was reportedly spotted smiling and celebrating when Sydney FC players began to celebrate at full time.
The ballboy incident was momentarily overshadowed by Sydney FC star Michael Zullo's classy gesture to give his FFA Cup medal to the ballboy.
Marrone is potentially facing further punishment for his "bear hug" and could be hit with an additional match suspension.
Adelaide coach Marco Kurz apologised to the ballboy in a post-match interview.
"I said sorry to the boy and his Dad - what happened was not in the character of Mickey, he is a very quiet boy," Kurz said.
"In this moment we can only say sorry. Mickey is very down, I think he spoke with the boy.
"It's not in his nature, but we will apologise for the club and the players."
The incident could not take the shine off Sydney's first FFA Cup victory.
In a wild night of football, Sydney FC had to rally in extra-time after Nikola Mileusnic levelled for the away side.
Milos Nikovic opened the scoring for Sydney FC before Bobo's 11th minute strike proved to be the difference.
Sydney should have had their winner and more inside 90 minutes but for Reds keeper Paul Izzo's late heroics, saving a Bobo header at point-blank range and then denying the Brazilian striker again two minutes later.
Despite a late Sky Blues penalty appeal when the ball struck Marrone's arm in the box, the contest wasn't done in 90 minutes.
The Reds came agonisingly close to an extra-time winner, Matmour missing a sitter and substitute Mark Ochieng skying another with the goal and a first away Cup triumph beckoning.
But Bobo struck, and by the time Marrone was red-carded for manhandling the ball boy the match belonged to Sydney.
