Fofana, on loan at Union Berlin, was left fuming after being substituted off in the 70th minute of their 1-0 loss to Napoli in the Champions League.
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And upon leaving the pitch Fofana refused to shake the hand of manager Urs Fischer.
Footage showed the 20-year-old putting his head into his shirt when sitting on the bench.
Pictures then appeared to show the striker crying.
However, Fofana swiftly issued an apology to Fischer, his team-mates and supporters on his Instagram page.
He said: “Following my behaviour during my exit from the field, I wanted to apologize to the club, the coach, my team-mates and the supporters.
“This gesture was not intended and in no way does it represent my attitude, all this was generated as a result of frustration because I wanted to continue helping the team to obtain a positive result.
“We will continue to work and come back even stronger in the championship and in this great competition.”
After the game, Fischer explained the sub was made to keep his attack fresh.
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On the incident itself, he said: “There will be a talk. But I find it strange that this is the first question I get after such a great game from us.”
Fofana is yet to open his account for the German club, having now appeared in 11 matches.
He seemed to have registered an assist after a fantastic run from the right wing, before the goal was pulled back for offside earlier in the move.
The Blues announced the signing of the Ivory Coast international from Molde for £10.5million in December 2022, but he failed to score in four appearances.
Chelsea failed to qualify for any European competitions last year but appear to have finally found their feet this season under Mauricio Pochettino.
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