The Premier League champions were already at a numerical disadvantage after goalkeeper Thibaut Courtois was sent off for bringing down Bafetimbi Gomis, with the striker slotting away the resulting penalty to level the scores.
Chelsea were momentarily down to just nine men in the closing stages when the club's medical staff rushed to treat winger Hazard, who went down with a knock, meaning the Belgian had to leave the field.
And Mourinho, who reacted furiously at the time, felt their decision could have cost Chelsea the match in the final moments.
"I wasn't happy with my medical staff because even if you are a medical doctor or secretary on the bench, you have to understand the game," Mourinho said.
"If you go to the pitch to assist a player, then you must be sure that a player has a serious problem.
"I was sure that Eden didn't have a serious problem. He had a knock and was very tired.
"My medical department left me with eight fit outfield players in a counter attack after a set piece and we were worried we didn't have enough players left."
