The 39-year-old Brazilian, a reserve in the team that won a record fifth World Cup in 2002, had surgery on his right shoulder on Friday after suffering a training injury on January 15.
"I'll miss [football] a lot during those months that I'll be away from the fields but always thinking of returning," Ceni said in a message posted on his personal website.
"This is not the end, we've still got a lot of things to write together in this story," added Ceni, who reluctantly accepted medical advice to have the operation and plans to return in the second half of the year.
"We expect the goalkeeper to remain off the pitches for close to six months during his recovery," surgeon Sergio Schubert was quoted as saying on the club's website.
Ceni, most of whose goals have come from free-kicks with the rest from penalties, is the only player to have turned out more than 1,000 times for Sao Paulo and helped his club win three Brazilian championships in a row between 2006 and 2008.
Sao Paulo, who are playing in the Paulista state championship before the Brazilian first division kicks off in May, said former Sevilla striker Luis Fabiano would stand in as team captain during Ceni's absence.
