A late Junior Messias goal was wrongly cancelled out seconds before Emmanuel Gyasi's winner.
Referee Marco Serra later apologised to Milan players and Pioli said: “I tried to calm my players down, but I didn't manage as Spezia's goal proves.
“We knew it was an injustice, we have ourselves to blame, but we share responsibility with the referee. I am sorry to say that. He even apologised, maybe that wasn't even a fault. It's a shame.
“However, we should have scored more goals in the first half, it's a bad night and we must react now."
Theo Hernandez missed a penalty kick in the first half.
“We could have won the game, somehow we lost and it's heavy," the coach continued. “We knew we had a good chance, Leao's goal should have given us self confidence, we failed to seal a win that we strongly wanted, but the season is still long."
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