The two centers sparked a brawl after Embiid trapped Towns in the corner on a double team, locking arms and shoving each other at Minnesota's end of the floor.
Towns ended up throwing a punch at Embiid and missing before putting the Sixers' big man in a headlock. Ben Simmons also took part in the fight, appearing to have his forearm around Towns' throat.
Teammates and coaches separated Towns and Embiid before both were ejected from the game.
Despite the Timberwolves' rejecting the officials' claim that Simmons was a "peacemaker" in the brawl, all parties ultimately deemed that he was trying to calm the fight.
"While we are disappointed in the league's decision, we understand the magnitude of this unfortunate incident," Timberwolves President of Basketball Operations Gersson Rosas said in a statement. "The NBA is highly competitive and last night was a reflection of that. We support Karl and will move forward together as a group."
Simmons was not fined by the NBA.