Rypien was 23-of-43 passing for 331 yards and Alex Mattison had career highs of 242 yards rushing and three touchdowns for Boise State (8-2 overall, 6-0 Mountain West).
Rypien's lone interception, with six minutes left in regulation, set up Rashaad Boddie's 4-yard touchdown run that gave Colorado State (6-5, 4-3) a 52-38 lead with 2:58 to go. Rypien led the Broncos on a 10-play, 75-yard drive that was capped by his 13-yard TD pass to Sean Modster just more than a minute later.
Boise State wide receiver Cedrick Wilson recovered the ensuing onside kick and, five plays later, Rypien hit Jake Roh for a 6-yard score to tie it with 57 seconds remaining and force overtime.
After a pair of 3-yard runs by Mattison, on third-and-4, Rypien connected with Roh for 15 yards to set up a 4-yard TD run by Mattison that made it 59-52. Then, on third-and-2 from the 6, Leighton Vander Esch forced a fumble by Boddie that Boise State's Tyler Horton recovered to seal it.
Colorado State scored touchdowns on each of its first five possessions to take a 35-10 lead into halftime.