Tomori was given a straight red card in the 18th minute for a last-man foul preventing a goal scoring opportunity on Mason Mount who won a penalty too.
The ex-Chelsea defender tugged on Mount’s shoulder twice, suggesting it was a spotkick, but the red card appeared harsh given the midfielder didn’t have the ball under control.
“I don’t need to see the replay, it was too easy to judge that incident,” Pioli told Mediaset after the game.
“I told the referee what I thought of him after the match. My English isn’t exactly fluent, but I think he got the general idea.
“The game had just started and I had the feeling we were doing well. The red card and penalty changed the game, against a team that was already strong and did not need to have an extra man too.”
Jorginho converted the 21st minute spotkick, before Pierre-Emerick Aubameyang added a second in the 34th minute.
The result puts Chelsea in top spot with seven points in Group E, ahead of Salzburg who drew 1-1 at Dinamo Zagreb. It leaves Milan third in the group with four points from four games, after back-to-back defeats to the Blues.
“It’s a negative result, but our destiny remains in our hands,” Pioli said.
“If we want to be competitive in Europe too, we need to win the next two, and we have every chance of doing that We paid a very heavy price for one incident.”
Chelsea boss Graham Potter added: “The red card changes the complexion of the game but we still have make their 10 men count, which I think we did quite well.”