First-half strikes from Alhassane Bangoura and Leo Baptistao saw Vallecano to victory against their local rivals, who now lie 12 points behind Barcelona after suffering their second loss in three league matches.
Atletico remain the closest challengers to the leaders, but Simeone was less concerned about their title hopes than he was about their performance overall.
"In the first half we did not play well," the Argentinian said on www.clubatleticomadrid.com.
"We improved in the second and I think we had chances to win, but in the first half they were the better team and we found ourselves 2-0 down.
"Rayo played well and you have to give credit to the opponent. They started better than us, they were more dynamic, more efficient and got the early goal.
"Rayo got off to the better start, they played very well, with great intensity, with people coming in from the wings with speed."
With their title hopes fading, Simeone has now tasked his players with improving on last season's fifth-placed finish.
"We do not look at how the league will end," he said. "We want to improve on what we did last season.
"The league is very long and it's how it ends. Want to finish as high as possible and improve on where we ended last year."