Minnesota athletic director Joel Maturi confirmed the decision Sunday night.
Kill went 23-16 and led the Huskies to bowls in all three of his seasons there. Northern Illinois went 10-3 this season, including a 34-23 victory at Minnesota that laid the groundwork for Gophers coach Tim Brewster to be fired.
Minnesota went 3-9 and 2-8 in the Big Ten this year. Brewster was fired in October after the team started 1-6 in his fourth season on the job. Interim coach Jeff Horton finished the season with wins over Illinois and Iowa.
Kill went 6-7 in his first year in DeKalb, Ill., and 7-6 last year before the breakout season in 2010. The Huskies lost to Miami of Ohio in the Mid-American Conference championship game on Friday and were ranked as high as No. 24, the first time Northern Illinois has been in the AP Top 25 poll since 2003.
Kill will not coach Northern Illinois in the uDrove Humanitarian Bowl against Fresno State on Dec. 18 in Boise, Idaho. Athletic director Jeff Compher said he has not yet determined who will coach the team or which members of the coaching staff will remain for the bowl.
Compher was informed within the last 24 hours that Minnesota was interested, and Kill would be leaving. But even that did not blindside him because of the success Kill has had at Northern Illinois.
"He'll bring the same skills that he brought here, that hard hat mentality," Compher said. "He'll work hard on the recruting trail, he'll have a great relationship wtih players. ... He will do a fantastic job."
Kill inherits a program in shambles.
Maturi made a big gamble when he hired Brewster, a tight ends coach for the Denver Broncos at the time who had no previous experience as a head coach or coordinator in college or the pros, to take over for Glen Mason.
It was a disaster from start to finish. Brewster went 0-10 in trophy games, butted heads with Maturi on several occasions and wasn't able to capitalize on brand new TCF Bank Stadium, a shimmering $300 million project that was supposed to put the once-proud program back on the map.
Brewster's lack of success quickly took the shine off the wonderful new stadium, with the student section half-empty for most games and a lack of energy and excitement that was supposed to have been created when the Gophers moved back to campus after more than two decades of playing in the Metrodome.
At the press conference to announce Brewster's firing on Oct. 17, Maturi acknowledged the mistake and said one of the biggest selling points the university had for the new coach was, "You're not following Vince Lombardi here."
"This is a situation where, you know what, somebody can come in and win some games and people are going to feel good about him and they win a few more games and they're going to feel really good about him," Maturi said then. "And if we go to the Rose Bowl, we might even put a statue of them outside of TCF Bank Stadium."
He promised to attack the process with vigor and said he wanted to make a "Tubby Smith-type hire," referring to getting the big-name basketball coach away from Kentucky three years ago.
Head coaching experience was a must this time around after the Brewster move failed so badly, but Kill doesn't bring the big-name recognition that some of the initial names mentioned -- Boise State's Chris Petersen, Mississippi State's Dan Mullen, former Tennessee coach Phil Fulmer and former Oregon coach Mike Bellotti -- brought to the table.
Former Texas Tech coach Mike Leach openly campaigned for the job, but the Gophers never strongly considered him.
Kill went 4-5 in playoff games while coaching at Southern Illinois and 0-2 in bowl games with Northern Illinois. His head coaching career started at Saginaw Valley State in 1994 and went through Emporia State and Southern Illinois before he landed at Northern.
"No. 1, I'm ecstatic for Jerry," Northwestern coach Pat Fitzgerald said. "We've gotten to know each other pretty well over the years. The success he's had, his family, his background ... I'm ecstatic for him.
"I'm not happy because he's an outstanding coach [coming to the Big Ten]. That's great."
ESPN.com's Andrea Adelson and Adam Rittenberg, ESPNChicago.com's Scott Powers and Associated Press contributed to this report.