Ronaldo scored the opener before Gonzalo Higuain sealed the win late on as the Turin club booked their spot in the last 16 by finishing top of Group D.
But the former Real Madrid man was left irate as the pitch invader
Ronaldo expressed his displeasure by throwing his arm in the air in disgust and holding his neck as he walked away.
Stewards descended on the field and escorted the fan away, and it looked as if Ronaldo shouted, "Are you crazy?"
It was the second time Ronaldo was targeted by a pitch invader, having narrowly avoided one earlier in the game.
Juventus had already qualified for the next round of the Champions League, but Maurizio Sarri opted to play his big guns for the game.
Cristiano Ronaldo has nine goals from his 18 matches across all competitions for the Italian giants in 2019-20, with seven of them coming in the league.