Returning to the club where he established his reputation before moving on to represent Liverpool, Chelsea and AC Milan, striker Torres had a largely quiet game and was substituted after an hour.
But Atletico were impressive and deserving winners against the cup holders, with the advantage at the midway point of the last-16 tie earned by second-half goals from Raul Garcia – a penalty after he was brought down by Sergio Ramos – and teenage defender Jose Maria Gimenez.
The adoring Vicente Calderon crowd willed Torres on to the form that at one stage made him one of the world’s most feared strikers.
Ramos almost scored after just a minute when his header from James Rodriguez’s corner was pushed away by Atletico goalkeeper Jan Oblak.
Gareth Bale netted a 13th-minute glancing header that was ruled out correctly for offside.
At the other end of the pitch Raphael Varane made a perfect sliding tackle, atoning for his error in giving away the ball, to thwart fellow Frenchman Antoine Griezmann just as the Atletico frontman prepared to take a strike at goal.
A big chance arrived for Bale in the 52nd minute but he volleyed Marcelo’s cross wide with his right foot and with little conviction.
Atletico were awarded a penalty in the 56th minute, after Ramos clawed determinedly at Garcia’s shirt. Garcia took the spot-kick responsibility and found the bottom-right corner.
Torres made way soon afterwards, replaced by Koke.
Real made a change they hoped would transform the game as Cristiano Ronaldo was summoned from the bench. He lined up one free-kick but sent it 20 yards wide of goal – a mystery whether it was intended as a shot or cross.
It was 2-0 in the 76th minute, a powerful header across goal from 19-year-old Uruguayan Gimenez finding the top-left corner, and Real had little left to offer in response, pinning their hopes on transforming the tie in the second leg at the Bernabeu on Thursday, January 15.