Hamlin, who was left with a pounding headache and feeling sick by a combination of carbon monoxide and hot temperatures in the first Car of Tomorrow race last Sunday, put his Joe Gibbs Racing Chevrolet Impala on the point in the second straight COT race.
Hamlin's lap at 95.103 mph knocked Jeff Gordon off the top spot early in the qualifying session on NASCAR's smallest, tightest track, and Jamie McMurray later knocked him out off the front row with a lap at 94.955 mph in a Ford Fusion.
Gordon, the series points leader and a seven-time winner on the 0.526-mile oval, was seeking his seventh career pole here, but settled for the inside of the second row.
One week after Gibbs put two drivers in the top 10 in qualifying, the owners' three cars all qualified in the top seven with J.J. Yeley fifth and Tony Stewart seventh.
The pole is the fifth of Hamlin's career and first this year.
He said he learned last week while leading the race at Bristol that being out front in the new cars is a big help, which makes starting first especially important.
"It was a big, big deal with these cars," he said. "They punched such a big hole. Air around that track just really got disturbed and it seemed like once we got out front, we could just check out. If we were third or fourth line, we were really tight."
McMurray hopes for the same experience on Sunday in the Goody's 500.
He also was early in the qualifying order, but said he watched the drivers before him and saw several of them appear to overdrive their cars in the tight turns.
McMurray's got two good qualifying runs in a row in the CoT; last week, he started fifth.
The top 10 also includes Ken Schrader, who needed to make the field on time and drew cheers when his put the popular Wood Brothers Ford on the second row. Until a few years ago, the Wood Brothers team maintained its race shop in nearby Stuart.
Other Chevrolets in the top 10 include the Gibbs cars, Kevin Harvick in the No. 6 position, Dale Earnhardt Jr. in eighth and Johnny Sauter in 10th. Carl Edwards is the only other Ford in the top 10. He'll start ninth.
Six drivers who attempted to qualify did not. Among them were Brian Vickers, who burned his foot and suffered carbon monoxide poisoning last week while running 15th at Bristol, and Ward Burton, who crashed his primary car in practice and went to his backup. Also out was Michael Waltrip, the penultimate driver to attempt to make the field, who has not qualified in his Toyota since finishing 15th in the Daytona 500.