Stewart, who is one the 12 drivers in this year's Chase for the Sprint Cup championship, turned a lap at 191.959 mph around the 1.5 mile track for his 13th career pole but his first since August 2010 at Pocono. His lap time was only 0.006 seconds faster than title contender Kenseth and just 0.013 seconds ahead of third-place qualifier and current points leader Carl Edwards.
It's the first pole for Stewart in 26 attempts at Charlotte. He won the first fall nighttime race here in 2003.
"That was a [Ryan] Newman lap there," Stewart said. "We've been pretty solid since we unloaded, so it's a perfect way to start the weekend so far."
A.J. Allmendinger and Greg Biffle -- both non-Chase drivers -- rounded out the top-five.
Jimmie Johnson, the five-time defending Sprint Cup Series champion, took the ninth spot. Johnson picked up his second win of the season last Sunday at Kansas. He is a six-time race winner at this track.
Trevor Bayne took the tenth spot.
Other Chase drivers and their starting positions include: Kevin Harvick (14th), Dale Earnhardt Jr. (15th), Kurt Busch (20th), Jeff Gordon (23rd), Kyle Busch (25th) and Brad Keselowski (26th). Harvick won the 600-mile race at Charlotte in May.
After high speeds were posted in practice, teams were anticipating faster laps during qualifying. That wasn't the case.
"I thought we could pick up time, but it was kind of weird because we were watching the lap times, and guys weren't picking up as much as we are used to seeing here at Charlotte," Stewart noted. "I knew Ryan would put down a good lap, and I rely on Ryan a lot when it comes to qualifying, because he's the master at it for sure. We just took some information that he gave us and went forward."
The margin of time among the 43 drivers who qualified for this race was less than less than 0.8 seconds.
Teams will practice again on Friday afternoon. The 500-mile race at Charlotte is scheduled for Saturday at 7:30 p.m. (et).