"This was not an unexpected outcome," USC Athletic Director Pat Haden said. "We will comply with all requirements mandated by the result of this BCS vote."
The season will not have a champion on the record.
BCS officials had said USC was in danger of having its championship vacated after the Trojans were hit with heavy NCAA sanctions last year for rules violations committed during the 2004 and '05 seasons.
USC appealed the sanctions, which included a two-year ban from postseason play and a loss of 30 scholarships over three seasons, and the BCS waited until the NCAA ruled on the appeal to make a decision about its championship.
USC beat Oklahoma 55-19 in the Orange Bowl played on Jan. 4, 2005, to cap its perfect championship season.
The Associated Press contributed to this report.