The Kaulig Racing driver was one of three who still had a new set of tyres left when most pitted under a late Caution period, but scraped the wall and punctured one of them when the race restarted with 25 laps to go.
He would salvage a finish of 15th in the end while another of the above referenced three, Hendrick Motorsports’ Chase Elliott (#17 Chevrolet), won the 200-lap encounter by exactly half a second.
Brandon Jones (#9 Chevrolet) finished second and his JR Motorsports team-mate Sammy Smith (#8 Chevrolet), the other of the three who saved a new set of tyres, got home in third.
Van Gisbergen, who was arguably somewhat unfortunate in the incident which cruelled his hopes of a big result, did at least make up a handful of positions in the final laps in finishing 15th for a second race in a row in the #97 Chevrolet.
Cup full-timers Ty Gibbs (Joe Gibbs Racing Toyota) and Kyle Busch (#33 Richard Childress Racing Chevrolet) had shared the front row, the former choosing the high line and jumping into a clear lead over the latter.
Van Gisbergen had qualified 29th and essentially maintained position for the first 20 laps, as the top two put four seconds on the field.
Gibbs was at one point almost a full second ahead of Busch, who rounded up the #20 Toyota at Turn 4 on Lap 23, by which time Justin Allgaier (#7 JR Motorsports Chevrolet) was heading up the chase in third place.
Van Gisbergen had crept up to 24th by the time a Caution was called on Lap 31 after his team-mate AJ Allmendinger (#16 Chevrolet) and Riley Herbst made contact off Turn 2 which caused the #98 Stewart-Haas Racing Ford to spin into the infield wall.
Lots pitted, including the front-runners and van Gisbergen, meaning the order behind the Pace Car became Jesse Love (#2 RCR Chevrolet) from another Cup regular in Elliott, then Anthony Alfredo (#5 Our Motorsports Chevrolet).
Gibbs was fifth having jumped #33 in the lane, with Cole Custer (#00 SHR Ford) sixth, Busch seventh, and van Gisbergen back in 26th.
The restart came on Lap 37 and Gibbs pushed Elliott aside to reclaim the lead, with those who did not pit being no match for those on new tyres.
On Lap 42, Allgaier went underneath Gibbs to grab top spot at Turn 4, as van Gisbergen circulated in 22nd position.
When Stage 1 finished on Lap 45, Allgaier led Gibbs by 0.9s with Busch just behind, while van Gisbergen was scored in 21st.
The latter was 17th once a handful pitted in the break, after which the field re-took the green flag on Lap 53.
Allgaier and Busch moved into the top two from the bottom lane, while Gibbs had a huge scare when he slid up and scraped the wall at Turn 3, dropping to sixth.
Van Gisbergen dropped 10 positions in six laps, his cause not helped by those who pitted in the stage break coming through the field, while Allmendinger also lost ground after he bumped the wall upon the restart.
A Caution was called on Lap 72 in response to Parker Kilgerman (#48 Big Machine Racing Chevrolet) spinning off Turn 4, by which point Allgaier had been leading by almost a full second for several laps, with van Gisbergen having just crept back up to 27th from a low of 29th.
The front-runners chose to pit again, promoting Sheldon Creed (#18 JGR Toyota) and Elliott to the top two, and van Gisbergen to 14th, with 17th through 20th being Allgaier, Busch, pre-race series leader Austin Hill (#21 RCR Chevrolet), and Gibbs.
On the Lap 80 restart, Creed pulled clear from the bottom as van Gisbergen plummeted to 22nd on that lap alone.
That was largely due to the stoppers coming back through the field, with Busch charging to 10th outright on the restart lap.
Six laps later, though, he and Allgaier went underneath Creed to take first and second respectively.
Allgaier passed Busch for the lead off Turn 4 on Lap 87 and would win the stage by almost a full second, from Busch and Hill, with van Gisbergen 23rd at the end of Lap 90.
Almost all pitted in the break, with Allgaier and Hill leading them back out of the lane, only to be hit with speeding penalties and sent to the back.
Non-stopper Noah Gragson (#30 Rette Jones Racing Ford) assumed the lead, from Love, Creed, and Busch, while van Gisbergen took up 17th for the Lap 98 restart.
Predictably, Gragson sank like a stone, as Love bolted clear and Busch wrested second place from Creed.
Exactly halfway into the 200-lapper, van Gisbergen was 20th as Love led Busch by 1.1s.
The two-time Cup champion reeled in his team-mate and made the pass for first spot on Lap 108, as Car #97 ran in 22nd position.
A Caution followed almost immediately for a spin for Kyle Sieg (#28 RSS Racing Ford) at Turn 2 but, on that occasion, most stayed out.
Busch led from the bottom upon the Lap 114 restart and, after several battled for the top spots, it developed into a stoush between him and Sam Mayer (#1 JRM Chevrolet) for the lead on Lap 120.
By then, van Gisbergen had moved up to 15th position.
Mayer successfully pulled off a slide job on Busch at his second attempt, on Lap 127, while Gibbs had caught up to them.
On Lap 138, Mayer was two seconds to the good as SVG circulated in 16th.
The Kiwi was among the first in for a cycle of green flag pit stops, with Mayer peeling off from a three-second lead on Lap 147 but Busch running three laps longer.
Once it all shook out with 44 laps to go, Mayer led by 1.5s from Gibbs, then Custer, Jones, Allgaier, and Busch, with van Gisbergen 14th.
A Caution was called on Lap 168 for a Ryan Ellis (#43 Alpha Prime Racing Chevrolet) spin at Turn 2, and the ones to watch were Elliott in seventh, Smith in 11th, and van Gisbergen in 13th, given they all had a new set of tyres left.
Most pitted anyway, some for ‘scuffed’ (used) rubber, and the order for the restart was Gragson, Allgaier, Custer, lead pitter Mayer, then Gibbs, Jones, Elliott, Hill, Smith, Busch, Taylor Gray (#19 JGR Toyota), van Gisbergen in 12th, and Smith.
Gragson broke into wheelspin on the Lap 176 restart and cranked sideways when Mayer gave him a nudge as Allgaier threaded between them to take the lead.
Before Allgaier got back to the start/finish line, though, he was hard in the wall at Turn 4 after going across the nose of Gibbs, who had himself already bumped the barrier before #7 and #20 made contact.
Just behind, van Gisbergen had his scrape with the wall, the New Zealander looking to have already committed to the high line when Gray moved up and forced him even higher.
He was at least able to pit under Caution before the race restarted on Lap 183, but it was back under yellow again on Lap 184 when Custer and Hill came together.
Hill had slid up into Custer but appeared to take umbrage at the probability that he had done so because of contact moments which had cut a tyre, and made sure to unload the #00 Ford just as the Caution was called.
Elliott and Mayer shared the front row for the Lap 189 restart, with van Gisbergen 17th of 19 still on the lead lap.
Elliott and Busch led away from the bottom lane but the latter would soon cede second place to Jones, who gave chase to the #17 Chevrolet at the very head of the field.
The Hendrick driver was a full second up on Lap 191 before Jones closed in, and trailed by 0.485s at the white flag despite having not long scraped the wall.
Elliott would get the job done, though, by 0.500s, with Jones second from Smith, Mayer, and Allmendinger, who got onto barely used tyres in the closing stages, while Busch ended up sixth.
Van Gisbergen is back in a car in coming hours with Cup Series Practice from 17:05 ET/07:05 AEST, followed immediately by Qualifying.
VIDEO: van Gisbergen debriefs Charlotte NASCAR Xfinity race
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