The couple were married last weekend, Affleck's publicist, Rebecca Feferman, told The Associated Press on Monday.
No further information was provided.
Both are younger siblings of Hollywood notables: Affleck, 30, is the brother of Ben Affleck; Phoenix, 28, is the sister of Joaquin Phoenix and the late River Phoenix.
They pair became engaged in 2003. They have a 2-year-old son, Indiana August.
Affleck is now filming the movie, "Gone, Baby, Gone," directed by his brother Ben. His other screen credits include the "Ocean's 11" movies and 1997's "Good Will Hunting."
Phoenix has appeared on the NBC series "ER" and in the 2002 HBO movie "The Laramie Project."