Former Valencia player Samuel Lino and Memphis Depay struck to settle an encounter which Diego Simeone's team controlled. Victory took them ahead of champions Barcelona, fourth, on goal difference, after the Catalans crashed to a 5-3 home defeat on Saturday by Villarreal.
Atletico trail league leaders Girona by 11 points after Michel Sanchez's shock title contenders won 1-0 at Celta Vigo earlier Sunday.
Atletico made a host of chances in the first half but only found the breakthrough deep in stoppage time. Lino finished clinically after Antoine Griezmann found him with a superb pass.
Depay added the second in the 57th minute with a diving header from Nahuel Molina's cross, after midfielder Koke sprayed the ball out to the right flank. Dutch international Depay nearly scored another with a wonderful flick over a defender and then a vicious dipping effort which landed on the roof of the net.