Larson's 133.324 m.p.h. fast lap, however, was thrown out following post-qualifying inspection.
Larson had held a one-point lead in the standings over Martin Truex Jr. after Saturday's race, which Truex won.
The Charlotte native, who leads the series with two wins, will attempt to notch another victory in Saturday's Overton's 200 at New Hampshire Motor Speedway (4 p.m. ET on NBCSN). Jimmie Johnson and Matt Kenseth are set to start on Row 2 after finishing third and fourth in qualifying on the Magic Mile, respectively. Hamlin was in a backup auto after damaging his primary in a crash during practice earlier Friday. Because of the penalty, Larson will start last for the second straight race.
Byron is in his first year of Xfinity Series racing. Two months after injuring his back at Kansas, Aric Almirola returns to the No. 43 Richard Petty Motorsports Ford. The No. 42 sat on pit road when the session went green because the auto failed pre-race inspection last week at Kentucky Speedway.
Wondering how Kyle Larson's auto passed pre-qualifying inspection but failed post-qualifying inspection Friday at New Hampshire? Truex posted a speed of 133.077 miles per hour.
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"I wish I could have him on the box on Sunday, but we will be strong these next few weeks", Larson said.
Hamlin set the quick pace in his second lap of practice with a speed of 130.568mph in the back up auto. His top speed of 131.338 was exactly 29 seconds around the track.
Coors Light Pole victor Martin Truex Jr. backed up his show of speed Saturday morning in the second Monster Energy NASCAR Cup Series practice at New Hampshire Motor Speedway.
The on-track traction will come from the surface at NHMS being treated with PJ1 TrackBite, a type of resin that will be applied to the very bottom of the track on the yellow lane, and two lanes above the racing groove.