The loss marked the first time in 59 years that the Huskers have dropped three consecutive home games in one season.
After starting the season with a 2-3 record, the Northwestern Wildcats have now won four straight after defeating Nebraska by the final score of 31-24 in overtime on Saturday.
Lee then threw his first interception in his past 122 attempts on the ensuing drive, spotting the Wildcats' at the Husker 40-yard line. They traded scores in the first half, with the Wildcats leading 17-14 on a late Charlie Kuhbander field goal.
The "pick-six" came on the opening drive of the third quarter, helping the Huskers to their first lead of the game.
Nebraska's second touchdown of the game followed a similar script. Freshman tight end Jack Stoll's second-quarter touchdown reception was also his second catch of the season.
Nebraska scored a touchdown in the first quarter for the first time since late September versus IL. Kuhbander attempted a 45-yarder as time expired in the half, but he missed it wide left.
Thorson led the Wildcats 84 yards downfield and finished off the drive with a rushing touchdown on the 13th play.
Nebraska linebacker Marcus Newby had a 49-yard interception return for a touchdown on the third play of the second half.
Thorson, who completed 19 of his 35 passes and threw for 243 yards and two interceptions, tied the game on a seven-yard touchdown run with 5:33 remaining in the game.
Lee then converted two straight third downs with a 16-yard pass to Spielman and a seven-yard toss to De'Mornay Pierson-El to move the ball into Northwestern territory with just over a minute to play.
The Wildcats got the ball first to start overtime, and it took a gutsy fourth-and-goal from the one quarterback sneak by Thorson to take a 31-24 lead.