The Curva Sud fan group boycotted the clash at San Siro, where Milan claimed a much-needed 3-1 win to ease the pressure on under-fire coach Filippo Inzaghi.
Banners in protest of the way the club is being run were unfurled, with Milan sitting seventh in Serie A.
Dutch midfielder Marco van Ginkel said the absence of the fans was felt, and believes the players need to win them back.
"The Curva Sud weren't in the stadium today and we missed their support," Van Ginkel told the club's website.
"We need their support but we have to bring them back to the stadium and to support us."
A brace from Jeremy Menez and a Philippe Mexes goal helped Milan to their victory, ending a three-game winless run.
Milan defender Luca Antonelli said the supporters had every right to be upset about the campaign so far.
"The fans like us are disappointed about the season, but it's now down to us to bring as many fans back to the stadium," he said.
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