Coach Diego Simeone opted to leave Antoine Griezmann on the bench, cautious ahead of next week's Champions League quarter-final second leg at Leicester.
Atletico swept into the lead on 30 minutes when Belgian midfielder Yannick Carrasco drove the ball into the bottom corner from the edge of the penalty area.
It was 2-0 just after the start of the second half as Carrasco found the net again as he headed in a cross from Nicolas Gaitan at the far post.
Defender Filipe Luis added a third on the hour when he was picked out in the left side of the penalty area by Angel Correa.
Atletico missed the chance to further extend their advantage in a bizarre finish which saw two penalties missed during the final minutes.