Bonmati suffered the fracture during training with the Spanish national team on Sunday.
"Tests carried out on Monday... confirmed that she suffered a fracture... of the fibula on the left ankle," Barcelona said in a statement.
On Sunday, Catalan media suggested that she faced more than three months out if she needed surgery.
The three-time Ballon d'Or winner will miss Tuesday's women's Nations League final second leg against Germany and several matches for her club in the weeks ahead.
Bonmati started for Spain on Friday in a 0-0 draw against Germany in the first leg of the Nations League final.
She is set to miss upcoming Champions League games against Benfica and Paris FC in December, as well as the Spanish Super Cup in January and various Liga F matches.