The visiting manager at the Bernabeu refused to complain about the result and admitted that their rivals deserved the victory.
"I think Madrid played a very good game and we have to congratulate them. We couldn't find our way," Simeone told reporters after the game.
"Two goals came off the bodies of a player. There weren't many other big chances, but this was a great result for our opponent.
"We could not connect as we wanted, they pressed very well. Real Madrid are always strong. I've rarely seen them be less strong."
Atletico will look to overturn the deficit in the second leg next Tuesday.