City's Bernardo Silva and Mateo Kovacic both misfired in the shootout to put Madrid in the driving seat
The 28-year-old Spain international, who did not go to the World Cup, said on Monday he had broken a metatarsal in his right foot.
"I want to let you know that its going to be hard for the next few months, I fractured my fifth metatarsal and will be out a few months," Negredo wrote on his Instagram account.