Viacom owns MTV, VH1, Comedy Central and the Paramount movie studio, and is headed by Chairman Sumner Redstone.
Freston's departure comes only days after Redstone disclosed that Paramount was abruptly ending its 14-year relationship with Tom Cruise, saying the movie star's off-screen behavior was hurting box office returns.
Freston was said to be caught off-guard by Redstone's announcement, Variety reported last week. The trade newspaper also said that Redstone had not defended Freston after negative articles about him and his leadership of Viacom.
Freston, 60 and a founder of MTV, became president of Viacom in January when it split off its CBS television and radio into a separate company called CBS Corp.
Viacom also named Thomas E. Dooley to the newly created position of senior executive vice president and chief administrative officer.
Both Dauman, 52, and Dooley, 49, have held a number of executive positions at the company, including deputy chairmen from 1996 to 2000, and both currently serve on Viacom's board.
Since 2000, they have both run DND Capital Partners, LLC, a private equity firm specializing in media and telecommunication investments.
Dauman will report to Viacom founder and Executive Chairman Sumner Redstone.