The rebel group initially pushed into Bangui Saturday and fought its way through the capital Sunday to take control of the presidential palace, Voice of America reported.
It was not immediately known where Bozize had taken refuge.
Prime Minister Nicolas Tiangaye Saturday asked members of Seleka to get in contact with him to negotiate a peaceful solution and avoid a bloodbath.
The rebels had previously called for Tiangaye's resignation as prime minister as per a cease-fire deal in January that would keep Bozize in power. They accused Bozize of breaking the cease-fire agreement.
Seleka spokesman Eric Massi told Voice of America that Bozize must leave the country to bring peace.
Rebels began their offensive in December, taking control of about one-third of the country.
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