Third-placed Milan need a draw at fourth-placed Fiorentina to be sure of going directly into the group stage of next season's Champions League.
The defender, who helped Milan win Europe's top club competition win five times in his 24-year career, admitted he was upset.
"I was a wounded man," Maldini told La Gazzetta dello Sport. "The stadium was full of families and 70,000 people who were cheering me. It's a shame those 500 ruined the party."
"The club's silence (disappointed me)," he said.
"I didn't like it that no one took a position. From the president (Silvio Berlusconi) down, not one of the directors said a word. I think a club like Milan should disassociate itself from certain episodes."
The player said he did not know why the group of 'ultra' fans had staged the protest.
He speculated it might have been prompted by a heated exchange with fans at the airport returning from Milan's 2005 Champions League final loss to Liverpool or comments he made in 2007 criticising some 'ultras' for failing to support the team.
Sunday's match in Florence may also be the last one at Milan for coach Carlo Ancelotti, who is being linked to Premier League Chelsea.
Luis Figo may bow out too in champions Inter Milan's home game against Atalanta, as his contract is running out and he has not decided whether he will keep on playing.
Aside from Fiorentina and Milan's tussle for European positions, the only other issue to resolve on the season's last weekend will be whether Torino or Bologna go down to Serie B with Reggina and Lecce.
The two clubs both have 34 points but Bologna will stay up as long as they match Torino's result at Roma when they face Catania at home thanks to a better record in the head-to-heads.
