Diego Simeone started with five debutants, including the teenage forward, for Sunday's (AEST) trip to Estadio Municipal de Burgo de Osma.
But, after taking an early blow on his right hip, the €126 million($203.2 million) signing limped off the pitch in the 26th minute and went straight down the tunnel.
New signings Kieran Trippier, Mario Hermoso, Renan Lodi and Marcos Llorente also started while Joao Felix's replacement Angel Correa hit the post shortly before half-time.
Having made wholesale changes at the break, including sending on another new defender, Felipe, Atletico took the lead in the 69th minute.
Substitute Rodrigo Riquelme delivered a deep cross from the right wing that Vitolo tried to meet with a diving header, the ball appearing to bounce in off his left arm.
Ivan Saponjic, who like the club's record signing Joao Felix has joined from Benfica ahead of the 2019-2020 season, then made it 2-0 to the visitors.
Neat build-up play led to Toni Moya freeing Manuel Sanchez on the left wing, with his centre coolly converted by Serbian striker Saponjic for his first Atletico goal.
Atletico had finally found its rhythm and scored a third goal with six minutes to go, Felipe celebrating another debut goal for the Rojiblancos with impressive acrobatics.