Rodri is "out of the squad because of injury", said the Spanish national team in a statement, ahead of games against Georgia and Bulgaria on October 11th and October 14th, respectively.
The 29-year-old was taken off in the 21st minute of City’s Premier League win over Brentford on Sunday, confirming after the game he had felt discomfort in his hamstring.
Rodri was a key part of Spain's Euro 2024 triumph but suffered a serious knee injury in September of that year, missing the majority of last season as he recovered.
Spain did not say if they would be calling up another player in place of the 2024 Ballon d'Or winner.
On Sunday, coach Luis de la Fuente selected Celta Vigo striker Borja Iglesias to replace injured Barcelona star Lamine Yamal.