David Luiz was the victim of a reckless challenge from Sergio Aguero well into stoppage time, resulting in a fracas involving a number of players from each side.
Referee Anthony Taylor dismissed Aguero for his foul on the Chelsea centre-back, while Fernandinho also received his marching orders after shoving Cesc Fabregas during the ugly scenes.
No Chelsea players were sent off, though, and Conte was happy with his players' behaviour.
"The final [stage] was not good. I just hope David Luiz is not injured after this tackle," Conte told Chelsea TV.
"It is very difficult to explain this final part of the game. I support the referee. It is important that the referee whistles and we finish.
"I'm happy because I always tell my players to be focused on the game on the pitch and always to keep calm.
"It is normal when you play these big games it is not easy to keep calm in every single moment, but I am pleased because all my players tried to keep calm."
Chelsea had fallen behind to Gary Cahill's first-half own goal, but, after seeing Kevin De Bruyne somehow hit the crossbar from close range, the visitors roared back with goals from Diego Costa, Willian and Eden Hazard.