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Smith was leading the race when NASCAR threw a caution on Lap 69 for rain. The race was finally red-flagged after 79 of 100 laps and Smith declared the winner.
Smith grabbed the lead on a restart on Lap 65 when he went low on then-leader Corey LaJoie, who fell into the middle lane and dropped back in the field.
Tanner Gray moved into second at that point and the two were battling for the lead when the final caution came out.
Christian Eckes finished third, Colby Howard fourth and Grant Enfinger rounded out the top five.
Rounding out the top-10 were Ty Majeski, Tyler Ankrum, Corey Heim, Matt Crafton and Chase Elliott.
Travis Pastrana finished 13th in a career-best result for him.
“It’s huge. The past couple times I’ve actually been to Daytona I’ve gotten to visit Victory Lane. To do that for a third time is awesome.” Smith said. “I tried to play that race as smart as possible. When it was getting really aggressive, I’d get out of it.
“I knew these patches of rain were a thing but I didn’t think it would stick around for this long. I just wanted to be there after Stage 2 was over. You never know what’s going to happen.”
Smith isn’t done at Daytona yet. He will compete in Sunday’s Daytona 500, driving a third car for Front Row Motorsports.
“I’ll be out there Sunday,” he said. “It’s exactly how we started last year, so it’s looking good.”
Following the caution between Stages 2 and 3, most of the lead-lap trucks elected to pit with Crafton first off pit road.
On the restart on Lap 48, LaJoie led the way followed by Zane Smith, Heim, Matt DiBenedetto and Crafton.
Eckes, who restarted eighth, moved back into the lead on Lap 49. LaJoie got a shove into the top spot on Lap 50.
With 45 laps remaining, LaJoie continued to run out front, successfully blocking the advances of Zane Smith and Ankrum.
Rajah Caruth got loose in Turn 3 on Lap 58 while running three-wide to trigger a multi-truck wreck and bring out a caution. DiBenedetto, Friesen, Grant Enfinger and Daniel Dye were all involved.
Most of the lead-lap trucks elected to pit but LaJoie stayed out and in the lead. The race returned to green on Lap 65.
LaJoie fell into the middle lane and immediately dropped back on the restart, which sent Zane Smith into the lead.
NASCAR was forced to display a caution again on Lap 69 as it began raining once again. NASCAR ended up halting the race after completing 73 laps.
After about an hour, NASCAR was primed to restart the race and it even briefly returned to caution but the rain picked up again and it was halted against after 79 laps.
Stewart Friesen wrecked while leading the race on the last lap which brought out a caution and allowed Ankrum to claim the Stage 2 win.
Purdy ended up second, Crafton third, Nick Sanchez fourth and Eckes fifth.
Following the caution between Stages 1 and 2, the majority of the field pit but Ankrum stayed out and inherited the lead.
On the restart on Lap 26, Ankrum was followed by Friesen, Howard and Parker Kligerman. Friesen got a shove into the lead shortly after the restart.
Ankrum reclaimed the lead on Lap 27.
On Lap 29, Clay Greenfield and Gray got together entering Turn 1 which triggered a multi-truck incident that also collected Hailie Deegan, Daniel Dye, DiBenedetto, Dean Thompson and Bret Holmes.
The race was halted for nearly 12 minutes to allow crews to clear the track of debris. Several trucks pit during the caution. The race resumed on Lap 36 with Ankrum still in command.
Howard moved into the lead on Lap 37 but he got shuffled back as Friesen moved out front.
Eckes lost, then regained the lead in the final lap and a half, holding off Crafton to take the Stage 1 win.
DiBenedetto was third, Deegan fourth and Sanchez rounded out the top-five.
Sanchez, who started on the pole, got off to a slow start which allowed Majeski to lead Lap 1 but Eckes got a shove to the point on Lap 2.
The race was placed under caution on Lap 3 for light rain. A handful of trucks elected to pit and Derek Kraus was penalized for having a crew member over the wall too soon. The race resumed on Lap 7 with Eckes out front.
Just after the race restarted, NASCAR threw the caution again as rain started in Turns 3 and 4.
After a brief delay, the race returned to green on Lap 11.
On Lap 13, Crafton got a push past Eckes to take the lead for the first time in the race.
With five laps remaining in the stage, Eckes returned to the lead followed by DiBenedetto and Sanchez.