The three-time Supercars champion managed to finish on the lead lap when he received the free pass before the second and final Overtime restart, after which Ryan Truex overtook Carson Kvapil for victory.
Brandon Jones (#9 Chevrolet) had qualified on pole position and took the initial lead from the outside lane, with his JR Motorsports team-mate Justin Allgaier (#7 Chevrolet) rounding up Riley Herbst (#98 Stewart-Haas Racing Ford) for second by the end of Lap 1.
Van Gisbergen had started 31st and was running 29th in the #97 Kaulig Racing Chevrolet when a Caution was called on Lap 5 due to a crash involving JJ Yelley (#35 Joey Gase Motorsports Toyota) and Hailie Deegan (#15 AM Racing Ford) at Turn 1.
The restart came on Lap 14 an Allgaier took the lead from the bottom lane, with Jones slotting into second and Herbst rounding up Sheldon Creed (#18 Joe Gibbs Racing Toyota) for third.
Van Gisbergen essentially maintained position all the way from that point until the Lap 26 Caution for a fire for the #39 RSS Racing Ford.
Ryan Sieg was quickly out of the car and away from the scene under his own power, before being released from the infield medical centre during the yellow.
Van Gisbergen and a handful of others took the opportunity to pit with an eye to the Lap 45 stage finish, the highest-running of those being last-start winner Jesse Love (#2 Richard Childress Racing Chevrolet).
Love was 27th and van Gisbergen 32st for the Lap 33 restart, at which point Allgaier led the field away from the inside lane, with Jones slotting into second, from Creed.
Allgaier won the stage, from Jones and Cole Custer (#00 SHR Ford), with Love in 21st and van Gisbergen in 24th.
Blaine Perkins’ #29 Ford was taken behind the wall under Caution due to an electrical fire, with that car being the sister RSS entry of Sieg’s.
Meanwhile, Parker Retzlaff (#31 Jordan Anderson Racing Chevrolet) filtered to the lead having also ‘flipped the stage’, and he shared the front row with Love for the restart, while van Gisbergen was fifth.
Love moved in front when the field took the green again on Lap 52, while van Gisbergen had dropped outside the top 10 after about half a dozen laps.
The Kiwi continued to battle with a loose #97 Chevrolet and had slid to 20th on Lap 78.
Meanwhile, Custer was showing the speed which he enjoyed at the end of Stage 1, and he took the lead when he got a run on Love and then went under the #2 Chevrolet at Turn 2 on Lap 73.
Custer would win Stage 2 by 1.2s, with Austin Hill (#21 Chevrolet) claiming second, from RCR team-mate Love and Retzlaff, while van Gisbergen was classified 19th at the end of Lap 90.
Once the stage break pit stops were done, Custer led from Hill, Allgaier, Herbst, and Love, with van Gisbergen 17th.
The green flag flew on Lap 99 and Custer cleared out to a two-second lead in just four laps as Allgaier eventually saw off Hill in their battle for second place.
By then, van Gisbergen was 21st, and he continued to slip all the way to last of the 26 drivers on the lead lap on Lap 105.
Custer’s lead over Allgaier had stretched beyond three seconds by Lap 120, with little prospect for early pit stops given the threat of rain.
Allgaier had cut the gap to 1.0s after 138 laps, thanks in part to traffic, by which time van Gisbergen had crept up to 23rd of 25 still on the lead lap.
On Lap 148, van Gisbergen did fall off the lead lap, although a pass on Kaden Honeycutt (#92 DGM Racing Chevrolet) in the process meant Car #97 held on to the free pass position for the time being.
He regained it soon after Jeremy Clements (#51 Jeremy Clements Racing Chevrolet) was lapped, but lost it again when Kaulig team-mate Daniel Dye (#10 Chevrolet) was passed by Custer on Lap 154.
That was crucial when a Caution was called due to rain on Lap 159, with 19 on the lead lap, Dye 20th, and van Gisbergen 21st.
By the time pit lane opened, the rain had eased and Herbst pitted from third.
Custer and Allgaier stayed out, although the former was supposed to pit but received the call too late.
A planned restart was delayed just as Sammy Smith (#8 JRM Chevrolet) rolled into pit lane from third place having apparently run out of fuel.
A red flag period followed on Lap 167, lasting around 15 minutes, after which Custer was straight back into a closed pit lane next time around for fuel and four tyres.
The #00 Ford dropped to 19th, leaving Allgaier and Hill on the front row, with the restart eventually coming on Lap 174.
Allgaier led initially but ran wide at Turn 3/Turn 4 and dropped to fourth, behind Hill, Kvapil (#88 JRM Chevrolet), and Creed.
A Caution came on Lap 175 when Jones spun at the exit of Turn 2 after receiving a touch from a loose AJ Allmendinger (#16 Kaulig Chevrolet).
Van Gisbergen had dropped to 23rd by then and it was Ryan Ellis (#43 Alpha Prime Racing Chevrolet) in 20th who received the free pass.
When the sixth restart came with 21 laps to go, Hill led Creed and Kvapil away from the green flag.
They were still the top three at the next Caution, called on Lap 184 when Taylor Gray (#19 JGR Toyota) whacked the wall exiting Turn 2 after a touch from Sam Mayer (#1 JRM Chevrolet) in their battle for fifth.
Van Gisbergen missed out on the free pass by four positions and was on Row 12 for the restart.
Hill struggled with traction when the green flag flew with 11 laps to go and Creed took the lead on the run into Turn 3.
Then Hill got into Creed’s left-rear corner at the start of Lap 191 and those two would be joined by Kvapil in a three-wide battle for first position.
Kvapil took over top spot, from Hill, Ryan Truex (#20 JGR Toyota), and Creed, before a Caution on Lap 194 when Herbst spun as a result of a touch from Allgaier.
Herbst’s #98 Ford was collected by the #28 RSS Ford of Kyle Sieg, who was among several backmarkers caught up in the crash.
That sent the race to Overtime, with van Gisbergen 20th and the first of those a lap down, but it was green flag running for just seconds given Hill spun at Turn 1 when Kvapil squeezed him tight.
That meant van Gisbergen finally did receive the free pass and he was again lining up on Row 10 for a second Overtime restart, with Kvapil on the high side of the first row and Truex on the low side.
Truex cleared Kvapil into Turn 3 and took the white flag before another incident further back brought out the Caution which decided the contest.
Creed snatched second from Kvapil, with Mayer, Custer, and Allmendinger rounding out the top five, while van Gisbergen was 18th of 20 on the lead lap after 208 laps.
The Xfinity Series now has a weekend off before resuming at Darlington Raceway on the weekend of Saturday, May 11 (local time).