Joao Felix netted twice - one in either half - to help secure the points for Diego Simeone's side.
Los Rojiblancos travelled to Pamplona without Luis Suarez or Saul Niguez as Simeone looked to rest a couple of his key players ahead of their Champions League trip to face Lokomotiv Moscow on Tuesday.
Joao Felix was handed the opportunity to open the scoring from the spot just before the break after Vitolo was brought down by Facundo Roncaglia in the penalty area. Despite the antics from Sergio Herrera in goal, Joao Felix kept his cool to give Atletico the lead.
When Simeone's men were awarded another penalty shortly after half time, Herrera won the battle of wits. Although he didn't save Joao Felix's spot kick, the Osasuna goalkeeper did unsettle the youngster enough for him to hit the post with his effort.
Joao Felix did eventually beat Herrera for a second time, thrashing the ball past the home goalkeeper when played through by Angel Correa in the 69th minute.
Atletico rallied the Osasuna storm, though, and found a third goal in the closing stages to guarantee all three points. Kieran Trippier found Lucas Torreira in the penalty area and the substitute powered the ball into the roof of the net.
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