Flowers, who scored 25 points in the second half, was named tournament most valuable player.
John Smith scored 18 points for Winona State (38-1), while Travis Whipple had 10 and Quincy Henderson scored 10 points with 10 rebounds.
A.J. Bowman scored 26 points to lead Augusta State (27-7), which was playing in the title game for the first time. He made 12 of 15 shots, an 80% rate that set a record for the championship game.
Winona State's Travis Whipple celebrates after the team beat Augusta State 86-76 to win the NCAA Division II men's college basketball championship in Springfield, Mass. Saturday, March 29, 2008. (AP Photo/Nancy Palmieri)