Diego Costa scored his second goal of the game with an acrobatic finish in the 81st minute to clinch a draw for the Blues.
Conte claimed that Fer's goal shouldn't have stood as the Dutchman fouled Gary Cahill in the build-up to the goal and heaped praise on his players for casting that aside to show character to force a draw.
Conte said: "The first goal, for sure, we must improve in some situations.
"For the second goal I think everyone can see the double foul on Cahill. It was a great mistake of the referee's but I also want to say this could happen for one side or the other side, I don't want to complain about this. It's the reality and it's a pity.
"I want to say after this situation we had a fantastic reaction. The players showed they didn't want to lose and tried to win until the end. I'm pleased with this.
"I also want to say if we have the opportunity to kill the game, we must kill it. We must learn this."