Diego Simeone turned towards his own fans and grabbed his crotch after Gimenez opened the scoring in a 2-0 win against Serie A Giants Juventus in their Champions League clash.
“It’s not a nice gesture I admit, but I felt the need to do it,” Simeone said.
“I did it as a player at Lazio and I did it again to show our fans that we have cojones. I can only apologise if anyone was offended.”
Juventus were also charged after the European governing body said their players arrived too “late for kick off”.
Atletico could also be facing further action for the behaviour of their fans, who are accused of throwing multiple objects and blocking stairways at Wanda Metropolitano.