The midfielder, on loan at Milan from Chelsea, was dropped to the bench for the Serie A clash at San Siro but was called on by Gattuso to replace Lucas Biglia, who went off midway through the first half.
When the coach went to ask the France international to replace him, Bakayoko did not seem to be ready immediately. The 41-year-old had a brief discussion with Bakayoko, which ended with the latter telling the ex-Milan and Rangers star to "f*ck off".
Gattuso then went on to speak to Jose Mauri, who took to the field to replace Biglia instead.
Bakayoko was reportedly left out of the starting XI in the first place because he had turned up an hour late for training on Wednesday.
But Gattuso said the air was cleared between the 24-year-old and his team-mates after he said he was sorry.
"We have settled our differences and he has apologised to the team. Everything is back to normal with him," said Gattuso.
"The training retreat was a difficult choice but there are rules to follow which are valid for everyone. We have to be aware of the team we play for and our values.
"In times of difficulty we all have to understand our responsibilities. We've been together at Milanello for about four days now and it has brought us closer together."
The 24-year-old has impressed since moving to Milan from Stamford Bridge, prompting suggestions from Gattuso and Paolo Maldini that the Italian side will pay the €35 million (£30m/$39m) needed to make his deal permanent this summer.
"At this moment we cannot do without him, he must remain at Milan," Gattuso said in February.
"He is proving his technical skills. You know that I am not in charge of the finances, but he is certainly giving us fundamental improvements.
"He can become an important player for this club for many years."
He has featured 39 times in all competitions for the Rossoneri, scoring one goal in Serie A.