The official Twitter account of Spain’s national team posted on Wednesday afternoon that Bellerin had been replaced by Sunderland’s loan full-back Javier Manquillo.
Bellerin was unable to finish training on Tuesday and has since been removed from the squad.
It is a second injury blow in just 24 hours for Arsenal, who are now also sweating on the fitness of Alexis Sanchez after he suffered a “low-grade muscle tear” in Chile training.
Concerns over Bellerin’s fitness were raised last week when he was left out of the Champions League squad to face Ludogorets.
But he returned to the Gunners line-up at the weekend, playing the full 90 minutes of the 1-1 draw with north London rivals Tottenham.
It is unclear whether Bellerin has pulled out of the Spain squad after the recurrence of an injury or whether he has picked up a fresh problem.
Earlier on Wednesday morning, the 21-year-old took to his Snapchat account to post a picture of his right ear.
The inside of the ear appeared to be seriously bruised – although there is no indication that was the reason he pulled out of the Spain squad.
It was revealed by Mirror Football on Wednesday that Bellerin has put pen to paper on a new six year contract at the Emirates worth over £100,000 per week.
City boss Pep Guardiola was desperate to get Bellerin and was hoping their shared Barca connections would help, but he has now committed himself to the Londoners.
Ozil, 28, and 27-year-old Sanchez are into the final two years of their contracts, and talks have begun on both.
Wenger is hopeful Ozil will sign and it is understood they are close on a contract with the German wanting close to £200,000-a-week on a five-year deal.