The teams combined for 83 points -- the most in Rose Bowl history -- but the Ducks (12-2) scored the final 10 points to win the Granddaddy of Them All for the first time since 1917. Thomas' 91-yard touchdown run was the longest in the game's history. He added a 64-yard touchdown scamper, while Darron Thomas threw for 268 yards and three scores.
"It's a statement," said Thomas. "They tried to put on our back that we couldn't win a BCS bowl game, but we came out, worked hard and made an emphasis that we weren't going to lose this game."
Wisconsin (11-3), meanwhile, fell in the Rose Bowl for the second consecutive year. Montee Ball ran for 169 yards and a score, tying Barry Sanders for the single-season FBS touchdown record (39) in the process.
The Badgers, who lost to TCU last year, took a 38-35 lead late in the third quarter on Nick Toon's 18-yard touchdown grab, then intercepted Darren Thomas on the Ducks' ensuing drive. But they couldn't hang on.
Senior quarterback Russell Wilson threw for 296 yards and a pair of touchdowns, but was intercepted by Kiko Alonso after the Thomas pick.
Oregon took over at the Wisconsin 39 and grabbed the lead six plays later on Lavasier Tuinei's 11-yard touchdown grab. A Badgers' three-and-out followed and Tuinei's eight-yard catch on 4th-and-6 extended a drive which ended in Alejandro Maldonado's 30-yard field goal, capping the scoring midway through the fourth.
Five plays into Wisconsin's next possession, Wilson found a wide-open Jared Abbrederis downfield, but Abbrederis was stripped while fighting for extra yards near the sideline and the Ducks' Michael Clay recovered at his own 27.
"I was fighting for extra yards," said Abbrederis. "I've got to be more careful with the ball but they made a good play on it, so my hat's off to Oregon."
LaMichael James then carried the ball six times before Jackson Rice punted it back to the Badgers with 16 seconds remaining. Wilson moved his team to the Oregon 25 with a pair of long completions before time expired.
It was evident from the start that this year's Rose Bowl would live up to its billing as an offensive slugfest. Wilson hit Abbrederis for a 38-yard touchdown on the game's opening drive and Darron Thomas responded on the Ducks' first possession, setting up James' short TD burst with a 35-yard pass to Tuinei.
Wilson then made it 14-7 with a four-yard scoring run. The teams traded punts before De'Anthony Thomas closed an explosive opening quarter with his record run, breaking through the line of scrimmage and sprinting 91 yards for a score.
Ball answered with a milestone scamper of his own, capping a 64-yard march with a three-yard TD plunge to give the Badgers a 21-14 lead.
Predictably, the advantage was short-lived, as Darron Thomas hit Kenjon Barner for a 54-yard touchdown on the Ducks' next play from scrimmage. The Badgers followed with a punt, but Mike Taylor made a diving strip-sack six plays later. The ball was recovered by Louis Nzegwu and returned 33 yards for a touchdown.
Oregon then reeled off an 87-yard march and Darron Thomas hit Tuinei for a game-tying TD seconds before the break. The teams' 56 combined first-half points set a Rose Bowl record.
De'Anthony Thomas, who only had two carries in the game, struck again three plays into the third quarter, getting the edge and rushing 64 yards to paydirt. Wisconsin answered with Philip Welch's 29-yard field goal and forced a three-and-out before grabbing the lead on Toon's TD grab.
Oregon lost the Rose Bowl to Ohio State in 2010. The school improved to 2-4 all-time in Rose Bowl games. Its other win came in the form of a 14-0 shutout of Pennsylvania in 1917...Wisconsin leads the all-time series with Oregon, 3-2...Thomas' 91-yard run bested the old Rose Bowl record of 88 yards, set by former Michigan running back Tyrone Wheatley in 1993...The previous Rose Bowl record for combined points was 80, set in 1991 in a matchup between Washington and Iowa.