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The New Zealander did not quite make it to Lap 30 of the 200-lap, third race of the season when he pitted with a reportedly overheating #97 Chevrolet.
Kaulig Racing pushed the car to its infield garage but van Gisbergen has not reappeared and is now officially out of the race due to an engine issue.
It completes a difficult weekend for the three-time Supercars champion, who qualified only 25th after Car #97 twice failed inspection.
Back at the initial green flag, Chandler Smith (#81 Joe Gibbs Racing Toyota) converted a front row start into an early lead, before a Caution was called on Lap 8.
Parker Retzlaff (Jordan Anderson Racing) had cranked sideways and while replays were inconclusive as to how the incident began, the whack in the side he then copped from Sam Mayer (#1 JR Motorsports Chevrolet) explained the left-rear damage to his #31 Chevrolet.
Van Gisbergen had slipped from 25th on the starting grid to as low as 28th in the opening laps but had inherited 24th under the yellow period.
Smith continued to lead when the race restarted on Lap 14 while van Gisbergen had slipped to 29th by the time he was into the pits on Lap 29 with his car reportedly overheating.
The #97 Chevrolet was pushed to Kaulig’s infield garage as Smith went on to clinch a dominant stage win when the first scheduled Caution of the evening came at the end of Lap 45.
Smith became the former race leader when a jack issue cost him six positions in pit lane during the stage break, and Austin Hill (#21 Richard Childress Racing Chevrolet) headed the field when Stage 2 went green on Lap 54.
Hill stayed there for a handful of laps before John Hunter Nemechek (#20 Toyota) moved past, and Smith made it a JGR one-two on Lap 62.
He continued to follow his team-mate until the final lap of Stage 2, when he went down the inside of Nemechek and made it two from two for the day.
Conditions were difficult for drivers, with the wind gusting to 70 mph (112 km/h), although whether debris caused van Gisbergen’s issue is not yet clear.
The season continues at Phoenix Raceway next weekend.
Update 11:27 AEDT
Nemechek has taken victory after grabbing the lead at the start of Stage 3 and not being headed thereafter (save for pit stop cycles).
Pole-sitter Cole Custer (#00 Stewart-Haas Racing Ford) took second and Smith, whose car lost pace after an adjustment during the Stage 2-Stage 3 break, got home in third.
