Fikayo Tomori was dismissed for a tangle with Mason Mount in the box as the Blues took a 1-0 lead after only 21 minutes of the Champions League clash at the San Siro.
Pierre-Emerick Aubameyang sealed the points before the break in a match that sparked fury among Milan commentators, with one moment involving Raheem Sterling also drawing ire.
The England winger was booked for a lunge on Rade Krunic before the half-hour mark and avoided a second yellow for a later incident involving Ismael Bennacer.
Former Serie A and Fifa-listed referee Graziano Cesari made clear his anger at the moment, and told Mediaset: “Sterling was rightly booked for a foul on Krunic, but then later the same player stopped Bennacer by not even looking for the ball. That was a red for me, absolutely.”
Milan boss Stefano Pioli admitted his team were “naive” in defence but expressed his disagreement with the decision to send off Tomori.
He said: “Of course there is anger and regret, we wanted to restart with a positive result but having to play 80 minutes outnumbered was a shame. We committed naivety on a defensive level.”
A number of pundits on Italian TV joined in with the criticism of Siebert.
Fabrizio Ravanelli, the former Juventus and Middlesbrough striker, stated on Mediaset: “The match never started, it was a decision that upset the challenge and the beauty of the match.
“Milan showed that they could put Chelsea in difficulty but the referee ruined everything.”