The Spain international suffered the injury in training this morning, delivering a blow to head coach Carlo Ancelotti.
Ancelotti had hoped to bring the playmaker into his team on a gradual basis in the early weeks of the season after he underwent groin surgery in June.
Alonso was not involved as Madrid began their league season with a 2-1 win against Real Betis on Sunday, and now his wait for first-team duty could be one lasting months.
Madrid announced in a statement on the club website: "The Real Madrid player, Xabi Alonso, has today suffered a fracture of his fifth metatarsal in his right foot according to the results of radiology tests he has undergone."
The medical examination was undertaken in-house, Madrid said.
Alonso's setback means he will miss Spain's World Cup qualifying match away to Finland on September 6, and casts doubt on whether he will return in time for the final two Group I games, against Belarus and Georgia, in October.