The coach grabbed his crotch after one of the goals and gesticulated to the fans, echoing a similar gesture he made during his playing days with Lazio.
Per Sky Sport Italia (h/t Football Italia), he explained he did this to show his fans his team has "cojones":
"I did it as a player in Lazio-Bologna and I did it again to show our fans that we have cojones. It wasn't aimed at the other team, I was turning towards our own supporters.
"It's not a nice gesture, I admit, but I felt the need to do it. It was such a tough game, we fought so hard and Diego Costa worked really hard when he wasn't 100 per cent fit. I had to show what I was feeling.
"I can only apologise if anyone was offended, but I did it from the heart."
Here's a look at the celebration:
Atletico were the better team in a defensive contest that burst open in the final 25 minutes. Jose Gimenez and Diego Godin both converted from set pieces to give the Rojiblancos a deserved win and put the team in a great position to advance to the next round.
The score could have been even more one-sided but the video assistant referee overturned a goal from Alvaro Morata for a light shove on Giorgio Chiellini. The Italian didn't put up much resistance, and Simeone did not like that call at all, per sportswriter Robbie Dunne:
But even without that disallowed goal, Wednesday's outing was a successful one for Atletico. Their defence is among Europe's best and is unlikely to concede three goals in Turin, which is what Juventus would need to knock the Spaniards out in regulation.
Atletico's great showing on Wednesday shouldn't come as a major surprise:
Simeone out-coached Massimiliano Allegri and found plenty of success with his substitutions. Morata, in particular, changed the match when he came on in place of Diego Costa, who was a surprise starter after only just returning from injury.
Costa was booked early and will out on the return leg on March 12, as will Thomas Partey. Alex Sandro will miss out due to suspension for the Bianconeri.