Feeney and Whincup were contenders throughout the majority of the Great Race, the latter having comfortably led across the first stint.
A poorly-timed safety car on lap 27 helped the sister Red Bull car of Shane van Gisbergen and Richie Stanaway get ahead, which led to double stacking issues later in the race.
Still, the #88 was able to fight its way into contention, with Feeney stalking van Gisbergen in the closing stages of the race.
That was until the car broke a gearshift tower less than 30 laps from home, ending their hopes of victory as well as denting Feeney's title hopes.
"I don't know what to say," Feeney told the broadcast.
"I'm gutted. We were really fast, the track was coming to us. I don't know what the fuel numbers are like but we were really fast out there.
"This place can be the best but it also can be the worst. I'm absolutely gutted."
A dejected Feeney did acknowledge that age is on his side for plenty of cracks at the biggest prize in Australian motor racing.
"It's all about the rollercoaster journey," he said. "I turn 21 in a couple of weeks so hopefully I get top come back and do this place plenty of times and have another crack at it. But man, it felt like it slipped through today.
"[Winning Bathurst is] the goal. That's what we were trying to do today. Obviously the [double] stack at the start didn't help and we fought back really well.
"I don't know what to say."
