Atletico led 1-0 when Costa and then Antoine Griezmann were brought off, drawing the ire of the home crowd when the French forward's opener was cancelled out by Portu moments after the latter of the two switches.
And although Simeone was disappointed that his side paid the price for their lack of firepower in the closing stages, he insisted he had little choice but to withdraw Costa.
"[Costa] had a knock and he wanted to come off after he continued for a few minutes," he explained, with Atletico confirming the forward will be assessed on Sunday.
Discussing the form of Griezmann, who was the subject of reported interest from Barcelona earlier in the day, the coach added: "[Griezmann] had a good match.
"He linked well with [Angel] Correa and Costa. Gradually, I think we are improving.
"I think we played well. We had control of the game and the equaliser came from a complicated situation. I think these are things that happen in the game; sometimes they are lucky and sometimes unlucky.
"I'm left with the feeling that this is a match we played well, but one where we lost two points."