The Portuguese was dismissed by referee Benoit Millot for dissent in second half stoppage-time of their 2-1 win over Brest in Ligue 1.
Fonseca was booked earlier in the match before seeing red and may now be set for a dugout suspension as a result of his reaction.
When Millot displayed the red card, the Portuguese boss marched up to the official and screamed in his face.
Lyon players were quick to intervene with some even pushing their manager away, but Fonseca decided to turn around and make his way back towards Millot.
Yet again, members of his squad stood between the two before two apparent members of security helped lead him away.
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Speaking to DAZN via RMC Sport after, Fonseca issued an apology for his behaviour that marred Lyon's home victory.
"I apologise for this gesture. I shouldn't do that. Football makes us do bad gestures. The match was very difficult.
"Playing against Brest is always difficult, they are a physical team, they defended a lot. These are very important points."
Lyon captain Alexandre Lacazette also said: "It's part of football. I think he'll regret this gesture but we'll see what the disciplinary committee says.
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"It's tension. There are a lot of questionable choices. When you live the match, sometimes you can do things. We're all behind the coach."
Fonseca, a former centre-back, started the 2024/25 season as the head coach at AC Milan.
However, he spent just six months at the San Siro and left the club eighth in Serie A at the end of December.
The 51-year-old was appointed at Lyon a month later, which sealed his return to Ligue 1 following a previous spell with Lille.
Victory against Brest was his third from five matches since completing his move and has them sitting sixth in the French top flight.
Lyon next face Romanian outfit FC Steaua Bucuresti in the Europa League on Thursday before a league clash at Nice, although Fonseca is set to be absent through his suspension.