Burton's performance included reaching a top speed of 195.194 mph on the 2.5-mile Daytona International Speedway track, two days after wrecking in the first qualifying race for Sunday's signature NASCAR event. He will start 39th.
Meanwhile, 2007 Daytona 500 champ Harvick clocked in with a 194.641 mph reading and claimed the fourth spot in the race.
Saturday's third-fastest speed went to Marcos Ambrose, followed by David Reutimann and defending Daytona champ Matt Kenseth.
Bobby Labonte spun out in the opening minutes of the qualifying race but avoided hitting anything.