The Badgers (8-6) won the coin toss in overtime and elected to play defense first. They pushed the Buffaloes (9-5) back, forcing a 45-yard field goal attempt by Pat Brougham that was pushed well right.
Wisconsin ran the ball up the middle three straight plays, setting up Allen's kick, which sailed through the middle of the uprights to give the Badgers a fourth straight bowl victory and seventh in eight tries under Coach Barry Alvarez.
Wisconsin tied it, 28-28, on a one-yard keeper by Bollinger with 51 seconds left in regulation. Bollinger completed two fourth-down passes on an 80-yard drive, including a 30-yarder to Darrin Charles to the Colorado one.
One play earlier, freshman Jonathan Orr got behind the defense but let a sure touchdown pass slip through his hands at the Colorado five.
Colorado trailed at halftime, 21-14, after Wisconsin converted three interceptions by Robert Hodge into touchdowns.
On Wisconsin's ensuing possession, running back Anthony Davis lost the ball after a hit by Medford Moorer, and the safety recovered the fumble at the Badgers' 17. Backup quarterback Zac Colvin threw an 11-yard touchdown pass to D.J. Hackett to give Colorado a 28-21 lead with 5:58 left in the quarter.
Brown left with a concussion early in the fourth quarter after rushing an Alamo Bowl-record 28 times for 97 yards.
Davis carried 26 times for 100 yards and a touchdown and Bollinger had 83 yards and a score on 19 rushes. Bollinger also completed 12 of 25 passes for 163 yards with two touchdowns and an interception.
Hodge completed six of 13 passes for 63 yards with a touchdown and three interceptions. Colvin was three of five for 15 yards and a score.
Colorado lost its second straight bowl game after winning its previous six. The Buffaloes fell to 4-1-1 all-time against the Badgers.