Kafka was injured midway through the second quarter. He'd been sacked and then completed a pass before he was replaced by Dan Persa. When he left, he'd completed 14 of 18 passes for 128 yards and carried eight times for 42 more.
Penn State trailed 10-3 in the second quarter when Kafka was forced out. And the Nittany Lions were still behind 13-10 at the half. But they shut out the Wildcats and Persa in the final two quarters and gave Paterno his 391st win.
"You got to understand that a kid like that quarterback is out of there, it's a big loss," Penn State coach Joe Paterno said. "Kafka's a heck of a football player. We played them more aggressively in the second half and did a better job with the pass rush, regardless of whether Kafka was in there or some other kid."
Persa, whose mother and sister attended Penn State, completed 14 of 23 passes and rushed for 42 yards on 14 carries, but couldn't get the Wildcats to the end zone. He was sacked four times.
There was no word on what type of injury Kafka had or how long he would be out. He was on the sideline during the second half and even pedaled an exercise bike, but did not return. He entered the game leading the Big Ten in passing yards and total offense per game.
"If he was healthy, I'd put him back in there," Northwestern coach Pat Fitzgerald said.
Information from The Associated Press was used in this report