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The three points took Diego Simeone's side up to fifth place, six points behind surprise leaders Girona with a game in hand.
"In the first half we were better, we controlled the game better, but in the second I think that fatigue made us lose strength," said Simeone.
Atletico dominated the opening period and deservedly took the lead in the 20th minute thanks to a left-footed drive from French international Antoine Griezmann.
Osasuna battled hard in the second half and thought they had equalised when David Garcia headed home in the 75th minute.
However, the goal was ruled out and Osasuna coach Jagoba Arrasate was sent off for protesting.
"It's a very clear goal, I told the referee and he sent me off," said Arrasate.
Rodrigo Riquelme hit Atletico's second goal in the 81st minute before a bad-tempered conclusion saw red cards for Atletico's Alvaro Morata and Ezequiel Avila of Osasuna.