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Los Colchoneros missed out on the chance to usurp Sevilla and go third in La Liga, as they struggled to break down their visitors after a thrilling first half.
Alvaro Morata's penalty and Joao Felix's deflected effort cancelled out Luuk de Jong's well-taken opener, before Lucas Ocampos' spot-kick - which he won - just before half-time earned Sevilla a deserved point.
With Atletico chasing a late win, the previously lively Joao Felix was taken off for former Sevilla winger Vitolo in the 80th minute, and the home fans seemed unimpressed by the alteration.
But Simeone stressed he felt it to be a necessary decision.
"We can't tell people that he felt overloaded in his calf," Simeone told reporters when asked to address the whistles that accompanied his withdrawal.
"The doctor told me to be careful with Joao because he was getting cramps, that's why the change came.
"That he scored a goal to make the people happy is normal, because he's from Atletico."
VAR attracted much attention during the match, as the two penalties came after lengthy reviews - Simeone felt the outcome of both incidents was fair.
"It ends up being more fair than unfair," he said. "I am far away from the play of the first penalty and very far for the second, so I cannot enter a summary.
"I don't think that the defining factor of the match was the VAR. It has been a good duel with two teams fighting for very high goals.
"We were two teams that have competed very well, and that will surely compete until the end for the Champions League [places]."
Sevilla coach Julen Lopetegui was less impressed by the use of VAR, however, particularly in terms of how long it took for the final decisions to be communicated.
"I believe that the VAR should intervene when situations are white or black," he added. "If you are waiting three minutes to see if you are going to review the decision or not, then that play is not very clear.
"There are many grey areas in football. That is what I meant. It should only intervene when it is black or white, because it cannot take so long, also because of the rhythm of the match, it stops too much.
"It was a very nice match. He [the referee] can't stand around for four or five minutes."