Milan agreed with the Italian Football Federation (FIGC) on a payment of 86,000 euros -- 33,000 euros per player and 20,000 euros for the club, Gazzetta Dello Sport and Sky Sport Italia reported.
The fine was cut by a third as AC Milan agreed to pay it immediately.
Acerbi had angered the Milan pair when he said there was "no comparison" between the teams before the game.
He said swapped his shirt with on-loan Chelsea midfielder Bakayoko "to put an end to the issue" but was furious when they held it aloft on front of Milan's fans afterwards.
Both apologised with the Ivorian Kessie, whose penalty sealed the win, insisting it was "just a joke, nothing more".
The match finished with scuffles on the pitch, with the two teams to meet again in the Coppa Italia semi-final on April 24 in the San Siro.
"A lot is being said about this incident, we got it wrong and have apologised. We can't do any more than this," Milan coach Gennaro Gattuso told reporters on Friday.
Meanwhile, a video of racist chants targeting Frenchman Bakayoko by a small group of Lazio fans during Wednesday night's 2-0 win over Udinese has circulated on social media.
Lazio fans can be heard in the video singing: "This banana is for Bakayoko".
The FIGC have decided not to open an investigation into the matter, according to reports.