While they had already sealed their qualification for the knockout stages of the competition, the Premier League leaders missed the chance to top their Champions League group on Tuesday (5 December) after they were held to a 1-1 draw by Diego Simeone's side.
Atletico opened the scoring in the 56th minute, with Fernando Torres flicking on a corner kick towards the back post when Saul Niguez was left unmarked to head into an empty net – having been allowed to spring free by Bakayoko.
The France international, signed from Monaco last summer, was replaced by Danny Drinkwater in the starting XI for Chelsea's last Premier League game against Newcastle United on Saturday 2 December and his midweek performance could see the former Leicester City midfielder return to the manager's starting XI for Saturday's league clash against West Ham United.
But Conte has come to Bakayoko's defence in the face of Wednesday's criticism, insisting he and the club will be patient with the 22-year-old.
"He is a young player, only 22. He is working to try to improve and go into our idea of football. It's important to have patience and understand mistakes during the game are normal, from every player," Conte said in his post-match press conference.
"My task is to try to improve my player, especially if a player is 22 years old. He has a lot of space for improvement. At the same time, I am very happy with his commitment and work."
Chelsea legend Frank Lampard was less forgiving of the French midfielder, accusing him of "sleeping" for Atletico's goal but hopes for improvement has he becomes more accustomed to English football.
"I don't know with Bakayoko," Lampard said while on pundit duties with BT Sport. "I think it's well documented that he hasn't settled quickly at Chelsea and English football in the Premier League as well and he has to come to grips with that.
"A moment's sleeping today doesn't work so he needs to improve but [Antonio Conte has] got options. [Danny] Drinkwater will play as well but hopefully Bakayoko will improve."