Biffle, who was the third to last driver to qualify in the 46-car field, turned a lap at 190.345 mph around the wide two-mile track for his seventh career Sprint Cup Series pole but his first since June 2008 at Dover (117 races ago).
His time was only 0.027 seconds quicker than Kenseth,
"Matt is becoming a hell of a qualifier," Biffle said. "I'm just so proud of the guys. They work so hard. Matt Puccia is a great crew chief, and he's really focused on these race cars. I just can't wait for Sunday.
Last month, Puccia replaced Greg Erwin as Biffle's crew chief on the No.16 Ford.
Biffle became the 15th different pole winner in NASCAR's top series in 2011.
He is currently 13th in points and has yet to win a race this season. Just four races remain before the Chase for the Sprint Cup championship begins.
"We have to win to get in [the Chase], and we feel like we can win here," he added.
Biffle has two wins at Michigan (August 2004 and June 2005).
Kenseth was the last driver to qualify since he posted the fastest lap in practice earlier in the day.
"I think I would've had a shot at the pole if I hadn't looked up at the [score] board," he said. "I watched Greg's lap, and I saw the lap time. I was thinking, 'That's really, really fast.' I got loose coming to the green flag, so I overdrove turn one to make sure I kept the car tight enough. I was glad to get a lap that good. I had a ton of speed."
It's the second time this season that Roush Fenway swept the front starting row, with the first coming in April at Texas.
Team owner Jack Roush has a track-record-tying 11 wins at Michigan.
Other notable drivers and their starting positions include: Kurt Busch (13th), Kyle Busch (17th), Tony Stewart (18th), Jimmie Johnson (19th), Carl Edwards (22nd) and Kevin Harvick (24th). Harvick won this race one year ago.
Sunday's 400-mile race at Michigan is scheduled to start just after 1:00 p.m. (et).