The Portuguese leapt well and steered a cross from Gabi into the top corner before the break and mid-way through the second half substitute Mario Suarez knocked the ball home from close range.
Antoine Griezmann could have given them a more resounding win five minutes from the end but his shot with the keeper Kiko Casilla beaten came back off the outside of the post.
Atletico moved up to fourth in the table with 17 points from eight games while Espanyol, who struggled against the home side's physical play, were down at 11th on nine points.
Diego Simeone's side have lacked the consistency, especially in defence, that won them the championship but they managed to keep a clean sheet following a 3-1 defeat away to Valencia in their last match before the international break.
"I think the team did what it had to do and was in control," Simeone told a new conference.
"We were playing in the opposition half with Raul (Garcia) and (Mario) Mandzukic in attack finding space as did Juanfran and Arda (Turan) on the wings.
"We were patient and the goal came. In the second half we were even more dominant."
Valencia are ahead of Atletico on goal difference and later take on Deportivo La Coruna while Sevilla, a point behind, are away at Elche.
Leaders Barcelona beat Eibar 3-0 on Saturday and Real Madrid swept aside Levante 5-0 as the pair warmed up for the El Clasico next weekend.
Image: Atletico Madrid's Tiago Mendes celebrates his goal during their Spanish first division soccer match against Espanyol
Photograph: Juan Medina/Reuters
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