"For the second time this year, you have a two-score lead in the second half and you can't get over that hurdle," Weis said.
Former Notre Dame quarterback Dayne Crist, whom Weis also coached with the Fighting Irish, was just 10 of 26 for 147 yards. He was sacked four times and missed wide-open receiver Kale Pick on a fourth-down play from the NIU 29 in the fourth quarter.
Asked whether Crist will remain his starting quarterback, Weis replied: "I don't assess that on game day. I think that you can make irrational comments. I do know that there are some throws that he'd like to have back that I'd expect him to make. That I do know."
Meanwhile, the Huskies (3-1) celebrated their 11th victory over a BCS opponent and their first since 2010 when they won at Minnesota. NIU players and coaches refer to those wins as "Boneyard" victories.
NIU coach Dave Doeren is a native of Shawnee Mission, Kan., and once served as an assistant coach at Kansas. But he downplayed any personal satisfaction.
"It doesn't mean anything from the Kansas part of it. Winning a BCS game is what that was all about," Doeren said. "Against Iowa in the opener (18-17 NIU loss), we didn't find a way to win. That's what we did (Saturday), find a way to win.
"I wanted that bad; I wanted a piece of history on our locker room wall. I never got to see a dog bone (symbolic of a BCS victory) with my signature on it. Now I have that. Being from Kansas and having worked there, that's great. But my mom's more excited about that part than I am. I'm just proud of our players."
The back-and-forth first half ended with NIU up 13-10, but James Sims' second touchdown run from 1 yard out put Kansas (1-3) on top 17-13 midway through the third period. Then Tyler Patmon picked off Lynch and returned the interception 54 yards for a score and a 23-13 lead early in the fourth.
From there, NIU took over. Recovering quickly from the interception 10 seconds later, Lynch flipped a short pass to Martel Moore, who out-sprinted the Jayhawks' secondary for a 65-yard touchdown.
"We saw the linebacker had been coming down all day on (Moore)," Lynch said. "He did a little slant behind him and I have the option of running or throwing. (Moore) was open, so I just threw it to him."
After a Kansas possession, Mathew Sims booted a 44-yard field goal with 7 minutes, 58 seconds left to tie the game 23-23.
Then, after a Kansas punt, Leighton Settle culminated a seven-play 53-yard drive with a 2-yard touchdown run with 4:33 to go and the defense did the rest to stop the Jayhawks on their last two possessions.