Alonso underwent an operation on a nagging groin injury in June and was expected to return in a friendly with Qatar's Al Sadd on Thursday.
However, the former Liverpool star now faces being out of action until mid November after breaking his fifth metatarsal in his right foot during training.
The 31-year-old has been the lynchpin in Real's midfield since joining in 2009, and his presence was missed in their opening game of the new La Liga campaign last Sunday when they scraped a 2-1 home win over Real Betis.
Real coach Carlo Ancelotti has plenty of cover in the midfield holding role, however, with Luka Modric and Sami Khedira plus new signings Casemiro and Asier Illarramendi.
Alonso is also set to miss Spain's next World Cup qualifier away to Finland in September, with the world and European champions leading Group I in their bid to reach next year's finals in Brazil.