Whincup executed two moves on Erebus co-driver Jack Perkins in the early stages of the race, one either side of the first stops, to set up yet another Sandown victory for Triple Eight.
Feeney inherited the car in a comfortable lead at the second round of stops and looked to be on for an easy win – only for a late restart to bunch up the field.
Feeney then held off series leader Brodie Kostecki to secure his first Sandown 500 win and a sixth for Whincup.
Kostecki and co-driver Dave Russell both contributed to the recovery of an early double stack that dropped them back into the pack to finish a fine second.
Will Brown made a late mistake to fumble a podium, handing third spot to Shane van Gisbergen and Richie Stanaway.
It was Whincup who made good early progress in the #88 entry, the veteran moving past Erebus co-drivers Russell and Perkins in the first couple of laps to lead the way.
Whincup was leading by about a second on lap 19 when fourth-placed Garth Tander's Grove Mustang shed its left-rear wheel on the way through the fast Dandenong Road section.
That left Tander beached in the turn 9 sand, prompting a safety car and a flurry of early stops.
There was even worse luck for James Moffat and Cam Waters, with Tander's stray wheel bouncing onto the back of their fifth-placed Tickford Mustang and tearing the rear wing off it.
Tickford managed to repair the car in time to keep it on the lead lap, while Walkinshaw Andretti United also used the caution to make running repairs to the back of the Chaz Mostert/Lee Holdsworth car after it sustained damage on the opening lap.
Perkins managed to jump back ahead of Whincup amid all the stops, while Russell went from being third to 10th in the order after being forced to double stack behind Perkins.
The race went green again on lap 26, Perkins initially leading comfortably over Whincup and Michael Caruso in the Team 18 Camaro.
That was until lap 39 when Caruso was easily passed by Porsche ace Kevin Estre, driving the #19 Grove Mustang, into turn 1.
Two laps later there was a change for the lead when Whincup eased past Perkins.
Once the magic lap 54 had been reached – the minimum for co-drivers – the second round of stops burst into life.
Perkins was the first of the front-runners to pit, handing his car over to Will Brown for the run to the finish.
Whincup and Estre, Broc Feeney resuming in a comfortable effective lead in the #88 as Matt Payne slotted back into third behind Brown.
Russell, meanwhile, had managed good progress during his second stint, moving into the top six before handing over to Brodie Kostecki, who found himself running fourth.
By half-race distance Kostecki was back on the podium after easing past Payne into turn 1.
Feeney made light of the third stint, pulling nearly nine seconds on Brown before the Erebus driver pitted from second on lap 87.
The Triple Eight driver then stopped two laps later, resuming in a lead over Brown that ballooned to more than 13 seconds over the 10 laps that followed.
Kostecki continued in third while Shane van Gisbergen used a long third stint to jump Payne for fourth during the third round of stops.
The fourth stint then saw Kostecki make ground on teammate Brown, closing to within a second as the race neared the three-quarter mark.
On lap 119 the fight between the Erebus cars was called off when Brown looked to let Kostecki through into second place as they blasted up the back straight.
Kostecki made his final stop on lap 125 followed by Brown on the following lap, the pair resuming in the same order as before the stops.
Feeney managed to execute his final stop with the lead intact, although his advantage over Kostecki was cut down to just over six seconds.
That margin was then erased entirely 20 laps from home when Cam Hill ended up beached at turn 9, sparking a second safety car of the race.
That led to a tense sprint to what became a time certain finish, Feeney leading with the two Erebus cars under his rear wing.
He was up to the task, though, withstanding the pressure to come home by just under a second.
Kostecki was second while Brown, who looked on for an easy third, made a costly late mistake at Dandenong Road. With three minutes to go he flew wide on the first left-hander, which allowed van Gisbergen through to snatch third place.
That capped off an incredible recovery drive for van Gisbergen and Stanaway, who came all the way from 19th on the grid.
It also keeps NASCAR-bound van Gisbergen's title hopes well and truly alive, although Kostecki did manage to increase his lead over the reigning champion to 155 points.
Feeney is now 204 points back in third, while Brown has lost more ground and is 294 points back in fourth.
Andre Heimgartner and Dale Wood made it an all-Camaro top five, while Payne and Estre were the best-placed Ford duo in sixth.
They finished ahead of Will and Alex Davison and Anton De Pasquale and Tony D'Alberto, with Tim Slade/Jono Webb and the T8 wildcard entry of Zane Goddard/Craig Lowndes rounding out the top 10.
The season continues with the Bathurst 1000 on October 5-8.
