However, substitute Barkley - a major injury doubt for the fixture - made sure Maurizio Sarri avoided his first league defeat as Chelsea boss by smashing home a rebound in the sixth and final minute of additional time.
"We are gutted. When you get yourself back into the game, not just back in the game but you are winning and concede with a minute to go, I'm still baffled where the referee got six minutes (of stoppage time) from".
"I did not get respect from the Chelsea fans", he said.
"I am not annoyed with anything". What happened was with Sarri's assistant, Sarri was the first one to come to me and say he will resolve it. "But then the young fellow came and he also apologised and I told him "I accept your apology, I also made mistakes especially when I was your age and try to improve".
However, both of those players were not involved in the latest England squad due to injuries and Barkley could now cement his place despite having only made 24 appearances so far in his worldwide career.
Antonio Rudiger had headed the hosts in front, but United turned the game around, Anthony Martial grabbing a brace in an absorbing contest between Mourinho's current club and one of his former employers. They came with a plan just to defend and play on the counter-attack. "I have spoken to a member of my staff and have dealt with this immediately".
Barkley's goal denied them the win, though, and led to the scenes at the end of the game that will nearly certainly prompt an investigation by the Football Association. "I will speak to him again tomorrow".
"We controlled that very, very well". Then after 1-1, we didn't play our football, only the long ball.
"Even though we were 2-1 down, we kept trying to score the equaliser and we did that in the end so I think the spirit was awesome", he added. Today I was happy with the performance for 60 minutes because for 60 minutes we played our football.
"It is not my reaction, it is Sarri's assistant", Mourinho told BBC Sport.
"The responsibility and the talk will always be about Pogba, but I'd rather talk about the other players".