Dillon, the 23-year-old grandson of NASCAR multi-team owner Richard Childress, became the became the fifth rookie driver to win the pole in the 56-year history of the race.
His performance also marked the return of Childress' No. 3 car, whose number had been retired since the 2001 Daytona 500, when driver Dale Earnhardt was killed in an accident during the final lap.
Earnhardt won six of his seven Cup championships while driving the No. 3 car.
Dillon, who claimed his first Sprint Cup Series pole, is last year's champion in the Nationwide Series.
Taking second place was Martin Truex Jr. with a lap at 195.892 mph.
The remaining spots in the 43-car field will be determined by Thursday's two Budweiser Duel races at Daytona.