"Congratulations on a wonderful moment," he said, according to press secretary Scott McClellan. "Tell the team congratulations, we're proud of them."
Brown got an early wake-up call from the president after a late night.
"You know your life is different when the first call you receive is from President Bush at 6 in the morning, and my wife Sally asks me, 'Can you take it,"' Brown said at news conference in Beverly Hills, Calif.
Vince Young scrambled for an 8-yard touchdown with 19 seconds left and the Longhorns beat the top-ranked Trojans 41-38 on Wednesday night, winning their first outright national championship since 1969.
The president apparently fell asleep during the game but woke up in time for the exciting finish.
McClellan said Bush wished Brown and the Longhorns all the best, and said that he looked forward to having them visit the White House soon.
Bush is a former Texas governor. His daughter Jenna is a UT graduate.