The seven-time Supercars champion returned to the series last weekend when he joined rookie Feeney in the #88 Holden for the Bathurst 1000.
While Feeney was listed as the primary driver and Whincup the co-driver, it was the recently-retired star that took the wheel of the car for Friday's wet qualifying session.
That decision came after Whincup was quicker than Feeney in the wet conditions in practice earlier in the day, T8 banking on Whincup as its best chance to get the car into Saturday's Top 10 Shootout.
As it turned out Whincup was only good enough for 14th in qualifying and the car missed the Shootout anyway.
Benching Feeney for qualifying was somewhat off-brand for Whincup who has been a fierce supporter of properly nurturing young talent since Feeney was floated as his replacement.
That comes from his own experience of being axed by Garry Rogers Motorsport after a tough rookie season back in 2003.
It also came after Whincup emphatically told media that, as the primary driver, Feeney would be responsible for qualifying the car when asked about it in the Thursday press conference.
Speaking to Motorsport.com after the Bathurst 1000, where he and Feeney finished fifth, Whincup acknowledged that the decision was out of step with his philosophy on nurturing young talent.
He explained that he had no part in the call, it instead falling to team manager Mark Dutton and engineering guru Jeromy 'JJ' Moore, while adding that Feeney himself backed the decision based on a lack of confidence in the conditions at the time.
When asked if the potential to undermine Feeney was considered, Whincup said: "It certainly was. The decision wasn't made lightly.
"I wasn't involved in the decision-making of that. It was Dutto and JJ. It was the engineering group.
"Broc wasn't confident in the car and he wasn't sure if it was the car or himself. He didn't know if he went 10 km/h faster over the top if he'd hang on or not, and he didn't want to test that out.
"So they threw me in for practice to validate that. If I had done the same thing, I would have jumped straight back out again. But [Craig] was quite quick, [Richie] Stanaway was quite quick – and it's not the place to learn, in a way. You've either got confidence or you don't.
"He was fine. He was happy [with the decision]. But it certainly wasn't my decision.
"And it wasn't my intention. I told the team we weren't doing the practice shootout. I've been here with equal pairings and there's a shootout in practice and the quickest gets to qualify.
"I didn't want any of that. I told the team that I'm the co-driver and Broc is qualifying the car. But when they didn't have any confidence over the top, they said they'd put me in.
"The idea was that I would get the car into the Top 10, and then he might have done the Top 10 Shootout. Especially if it was dry. But unfortunately we didn't get there."
