The Gophers (5-2, 1-2) snapped a two-game losing streak as James Manuel broke a 7-7 tie with a 24-yard third quarter interception return and Chris Hawthorne turned another Wildcat turnover into a 34-yard field goal in the fourth.
Host Northwestern (4-3, 0-3) dropped its third straight.
Kill, on indefinite leave after a series of epileptic seizures, watched Manuel picked off Wildcat quarterback Trevor Siemian with 1:22 for a go-ahead score. The Gophers made it 17-7 just 87 seconds later on Hawthorne's field goal after recovering a Wildcat fumble.
Hawthorne's 38-yard field goal with 5:24 remaining made it 20-10. Northwestern cut the deficit to 20-17 on a 10-yard touchdown strike from Siemian to Tony Jones with 2:07 remaining.
Gopher quarterback Philip Nelson was 8-of-11 for 112 yards, including a touchdown strike to Derrick Engel. Running back David Cobb rushed 20 times for 103 yards.
Siemian completed 25 of 46 passes for 234 yards but was picked off twice and fumbled once. Jones had eight catches for 84 yards.
Northwestern opened the scoring on Stephen Buckley's first career touchdown with 1:53 left in the first quarter. Buckley's 3-yard score capped a drive on which he had a 33-yard reception and an 11-yard run.
Minnesota tied the game at 7-7 as Nelson hit Engel hit on a 29-yard touchdown pass with 6:48 left in the first half.
Hawthorne's try for a go-ahead 44-yard field goal just before halftime sailed wide left.
Minnesota's defense shut down a promising Northwestern drive deep into Gopher territory early in the final frame. The Wildcats settled for a 35-yard Jeff Budzien field goal that cut the Gopher lead to 17-10 with 11:09 left in regulation.
After Hawthorne's second field goal, Northwestern converted on three fourth downs in a 75-yard scoring drive that culminated in Jones' 10-yard TD reception.
Two key Northwestern players were sidelined with reported ankle injuries: tailback Venric Mark and quarterback Kain Colter, who was dressed but only available in an emergency role.
Kill didn't coach for the second straight game but watched from a Ryan Field booth. Kill and his wife, Rebecca, drove down from Minneapolis and arrived just before the game. He reportedly addressed the Gophers at halftime.
Tracy Claeys has served as head coach in Kill's absence.
Minnesota hosts Nebraska next Saturday while Northwestern travels to Iowa.