The 67-year-old Belgian, who has served as IOC president since 2001, was the only candidate in Friday's election.
Rogge needed a simple majority in the vote, and the IOC voted 88-1 in favor of his re-election.
Rogge said after the vote that "you have given me a great honor. We have accomplished a lot together."
Brazilian IOC member Joao Havelange asked that the vote be done simply by acclamation, but Rogge insisted on a secret ballot.
Rogge was elected the IOC's eighth president in July 2001, defeating three other candidates and taking over from Juan Antonio Samaranch after 21 years in charge.