Maignan was closest to the Cagliari end and was celebrating with Tomori after the final whistle when they were allegedly subjected to racist abuse, which sparked a scuffle between players from both teams.
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"This Serie A matchday was dedicated to the stand against racism, but there's still a long road ahead and we must keep on fighting together," Milan tweeted after the match.
Pioli said both Maignan and Tomori told him they received racist abuse from the crowd.
"Mike told me it was possible to hear some insults from behind the goal," Pioli told DAZN. "It's the first time he reacted like that, so something happened. Tomori also told me the same thing.
"It's always sad when these things happen, nobody deserves that."
Cagliari striker Joao Pedro said he did not hear any racist abuse and defended the club's supporters.
"I didn't hear anything," he said. "That is a very delicate matter, but I was basically in midfield at the time.
"This is not a pleasant situation to talk about, but I have been here for eight years and I will defend the fans because I did not hear anything."