Neymar was shown a second yellow card the space of two minutes in Le Classique for knocking down Lucas Ocampos after the Argentine fouled him by the halfway line.
It was by no means the first time the Brazilian had been on the end of a rash tackle from a Marseille player, with Marco Verratti saying after the game he would have snapped long before his team-mate.
Neymar will miss PSG's home match with Nice on Friday through suspension, but that has not stopped Emery sending a clear message to Ligue 1 referees, despite speaking to the world-record signing about being provoked.
"He has to adapt to the league, to the team, to the referees," Emery told reporters. "He is intelligent and he is aware that he will learn from Sunday's game.
"Other players are aggressive with him, but it's important that the referees handle that. I talked with him about it, not responding to provocations, but players are people. They can react if there is too much aggression."
Emery has an embarrassment of riches in terms of attacking players at PSG this season, more so following the return to fitness of Javier Pastore.
But the Spanish coach reminded Pastore he will not find it easy to get back into the team.
"I'm happy with Javier," he said. "I want him to maintain this consistency without injury, that's important.
"I want him to be ready to play when the team needs him. There is more competition in the team at for his position now. By working every day, he will perform well when he plays with his qualities."
Emery also had a similar warning to Angel Di Maria, who is reportedly frustrated at being considered a rotation option.
The former Manchester United man has also suffered with injuries, including a thigh strain earlier this season, but Emery hinted at a potential starting role for him against Nice.
"He [Di Maria] is very competitive," Emery added. "When he doesn't play, he is not happy.
"He works to help the team. He wants to play every game, he always wants to start, but there is competition.
"He is ready to play, to enter the 11. I'm happy with his work. Friday may be a good opportunity for him. I'm sure he's ready."