Thorson scored on a quarterback sneak on fourth down that gave the Wildcats their first lead at 24-20 with 5:30 left in the game. He scored again on a short touchdown run four minutes later to seal the win.
Thorson finished 28 of 38 for 352 yards with two touchdowns passing and two rushing. He opened the scoring with a 33-yard touchdown pass to receiver Macan Wilson to give the Wildcats an early 7-0 lead.
Nevada answered with 17 straight points, highlighted by touchdown passes from quarterback Ty Gangi to McLane Mannix and Wyatt Demps.
Kicker Spencer Pettit hit a 31-yard field goal on Nevada's final drive of second quarter to send the Wolf Pack into halftime with a 17-7 lead.
Northwestern came out of halftime with a sense of urgency and put together back-to-back scoring drives. Thorson hit freshman receiver Riley Lees slanting across the middle for a 19-yard touchdown, tying the game, 17-17, with six minutes left in the third quarter.
Nevada was driving inside Northwestern territory early in the fourth quarter, before Wildcats defensive back Kyle Quiero made a leaping interception at the goal line to end the Wolf Pack threat.
Nevada responded with its own interception, when Elijah Moody picked off Thorson to set up the Wolf Pack on the Northwestern 17-yard line.
Nevada was forced to settle for another Pettit field goal, giving the Wolf Pack a 20-17 lead with 10 minutes left.
Gangi completed 16 of 37 passes for 199 yards with two touchdowns and an interception for the Wolf Pack, who dropped their opener under new coach Jay Norvell.
Northwestern star running back Justin Jackson finished with 109 yards on 30 carries.