The two Red Bull Ampol Racing Camaros were two of the three genuine contenders for victory in the 60th anniversary running of the Great Race, the other being the #99 Erebus Motorsport Camaro.
However, by the penultimate stint, Shane van Gisbergen was a clear leader and a one-two looked likely given Broc Feeney appeared to have the edge on Erebus's Brodie Kostecki, pending final fuel fills.
It left Feeney understandably shattered, while Whincup missed out on a podium as his co-driver but was able to enjoy seeing the sister car take victory in his capacity as Team Principal.
The Banyo-based squad started the day tied with the Holden Dealer Team for victories in Australia's biggest motor race, but is now officially without peer.
“I've always said this place is about the effort, and I couldn't be happier with everyone's effort this weekend,” he said.
“What you don't see from the outside is the grind that goes on for a full month before this event, let alone the huge week we embark on, but everyone played their role and did a phenomenal job.
“To have two cars in contention for a podium, if not a one-two, is just a true credit to everybody.
“It didn't go our way for #88 and I'm gutted for Broc and the #88 team because they deserved more after the fantastic week they had, but as a team we won the Bathurst 1000 so we should still hold our heads very, very high.
“To win this race is not about having the quickest car, it's about all the one-percenters and all the attention to detail to make this a great team.
“It's pretty special to win 10 Bathurst 1000s in 20 years. To come to this great race that's so easy to lose and to win 50 percent of the time is massive, and I couldn't be happier.”
After two stops for repairs, Feeney would take the chequered flag 19 laps down in 23rd when his first Bathurst 1000 silverware had beckoned.
“It was an interesting race,” said the 20-year-old.
“Jamie did a great job to get the lead off the start and pull a big gap. Things were going well and then we got caught with double stacking which put us a little bit behind.
“We stacked twice today but I think Jamie did an awesome job, he was motoring through the pack and got us back into the podium fight.
“We had a really fast car which was getting better and better, but I'm pretty gutted to finish the race in the pits.
“Everyone in the team has done a fantastic job this week and everyone should hold their heads very high.
“For #97 to get the win was fantastic, and although it's not the one-two we were hoping for, everyone should be very proud of what they did this weekend.”
Van Gisbergen had commiserations for Feeney as well.
“He's gutted, as he should be,” said the winner, post-race.
“He was fast all weekend and had a good chance for a one-two for the team today, in whatever order.
“It was a rough day for them with the stacking early, and then the recovery – what they were trying to do with the strategies to get back in front –it was pretty good.
“They never gave up, so yeah, pretty gutted.
“Gutting for the Supercheap guys as well, with the same failure.”
Craig Lowndes/Zane Goddard were last classified finishers at 20 laps down in 24th in the Supercheap Auto Camaro.
Lowndes does at least have seven Bathurst 1000 wins to his name already, including six of the 10 which Triple Eight can now boast.
It was back in 2003 that founding Team Principal Roland Dane led the mid-season acquisition of Briggs Motor Sport, with Lowndes and Whincup delivering the squad's first Great Race win in 2006.
That was the start of a three-peat, making them just the fourth and fifth drivers in history to achieve the feat, before Lowndes/Mark Skaife led Whincup/Steve Owen in a one-two in 2010, the first year of the ban of full-timers pairing up, and the team's first year with General Motors machinery.
Whincup and Paul Dumbrell added another victory for Triple Eight in 2012, before Lowndes and Steven Richards triumphed together in 2015 and 2018.
The 10th Bathurst 1000 victory for Triple Eight comes immediately after Feeney/Whincup achieved its 250th race win when they took out the Sandown 500, where van Gisbergen/Stanaway also got on the podium in third place.
SVG could yet win a third straight drivers' championship before he leaves Supercars for NASCAR at season's end, although he will have to overturn a 131-point deficit to Kostecki with two events to come in 2023.