"To avoid any risk whatsoever and safeguard the player's health, he has been released from the squad," said the EURO 2024 winners in a statement.
"Arsenal's medical staff have been fully informed of the entire process."
Zubimendi came on as a substitute in Spain's 3-0 win over Serbia on Friday.
The 27-year-old will miss Tuesday's friendly against Egypt in Barcelona.
Zubimendi has been a key part of Premier League leaders Arsenal's midfield this season, playing 44 times across all competitions.