Atletico revival under Simeone continues
The Uruguay defender bundled in from close range at a corner just before the break and forwards Adrian and Radamel Falcao missed gilt-edged chances to extend the lead.
Belgian goalkeeper Thibaut Courtois, on loan from Chelsea, kept the visitors in the game in the closing minutes with string of excellent saves as the Navarrans piled forward in search of an equaliser.
Under former Argentina captain Simeone, a huge fan favourite at the Calderon where he won a league and cup double as a player in 1996, Atletico have drawn once and won three on the trot without conceding a goal.
They climbed above Osasuna with 29 points from 20 games and are two points off a Champions League place. Osasuna are 10th with 27.
Atletico are 23 points behind city rivals and leaders Real Madrid, who beat bottom club Real Zaragoza 3-1 at the weekend.
Jose Mourinho's side opened up a seven-point lead over second-placed Barcelona, who laboured to a 0-0 draw at Villarreal.