Barnes shared the honor -- given annually to the nation's top NCAA or NAIA golfer –- with Oklahoma State's Hunter Mahan.
Barnes defeated Mahan in the finals of last year's U.S. Amateur Championship at Oakland Hills.
A senior at Arizona, Barnes also tied for second place at the Northeast Amateur and shared eighth at the Players Amateur.
Barnes put a scare into the best players in the world last month at the Augusta National, where he eventually shared 21st place. He also tied for 18th at the PGA Tour's Chrysler Classic in March.
"It means a lot to be named the top amateur player in college golf, but more importantly, to be associated with someone like Ben Hogan makes it more special," Barnes said. "He meant so much to amateur golf."
While he beat Mahan for the U.S. Amateur crown, Barnes also teamed with him to lead the United States to victory at the 2002 World Amateur Golf Championship.
The Ben Hogan Award is presented by The Friends of Golf and Colonial Country Club, in cooperation with Bank of America and the Golf Coaches Association of America. Barnes and Mahan will receive the award May 19 at Colonial Country Club.