Matt Kenseth qualified second after the two-round session at Daytona Beach, Florida with 196.036 mph while twice champion Dale Earnhardt Jr. took third, with 195.682 mph.
Reigning NASCAR Sprint Cup Series champion Kyle Busch (195.207 mph) and Roush Fenway Racing's Ricky Stenhouse Jr. (195.118 mph) rounded out the top five for NASCAR's season-opening event.
"This is a very, very cool day," Hendrick Motorsports' Elliott said in a trackside television interview after clocking the top speed.
"I don't know that this opportunity has sunk in yet, much less sitting on the pole for the Daytona 500.
"The big thing is just the team and Daytona 500 qualifying is about the team guys and the effort that they put into these cars. It was nothing special that I did, it's really just the kind of work they did this off-season to make it happen."
Elliott, who became the first rookie and youngest driver to win a NASCAR national series title at the 2014 Nationwide Series championship, has taken over the No. 24 Chevrolet from the recently retired Jeff Gordon, a three-time Daytona 500 winner.
"Opportunities like this don't come twice and I certainly want to make the most of this one," said Elliott. "This is very, very special and a very, very cool way to start our 2016 season."
Casey Mears was knocked out of the first round of qualifying by one-thousandth of a second by reigning Daytona 500 champion Joey Logano, who ended up qualifying in 12th place.
(Reporting by Mark Lamport-Stokes in Los Angeles; Editing by Larry Fine)
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