Kelly led the Ducks to a 12-0 record and No. 1 spot in the USA Today coaches' poll. Oregon finished second in the final BCS rankings and will play Auburn for the national championship in Glendale, Ariz., on Jan. 10.
Kelly is 22-3 in two years at Oregon, with a 17-1 record in the Pac-10 and two conference titles.
Chizik, who was named AFCA Region 2 Coach of the Year earlier Monday, was one of eight coaches up for the award along with Wisconsin's Bret Bielema, Michigan State's Mark Dantonio, Oklahoma State's Mike Gundy, Stanford's Jim Harbaugh, TCU's Gary Patterson and Boise State's Chris Peterson.
Kelly is Oregon's second winner of the award, joining Rich Brooks, who won it in 1994.
Terry Bowden is the only Auburn coach to win it, doing so in 1993.