The 25-year-old was poised to win his first cap for the European and world champions this month after committing his international future to La Roja.
However, the forward was forced to pull out of the squad after suffering a thigh strain in Atletico's 1-1 draw with Villarreal at the weekend.
"It is a pity for all the effort that he has been doing. He is eager to play with the national team. I want to emphasise the generosity of the player - another would go to the national team and expect to play," Simeone told COPE.
"He knows that Atletico has given him everything and he started by thinking about Atleti rather than his national team."
Costa has scored 13 league goals this season.