Whincup leads on 1847 points from Craig Lowndes (1800) and Will Davison (1792).
The V8 Supercar Championship has been thrown wide open heading into the most unpredictable part of the season following a completely out of character weekend by the most successful team of the current era.
A 12th different winner in season 2013 and failures by Red Bull Racing Australia's Jamie Whincup and Craig Lowndes has led to the tightest Championship battle in recent memory after James Courtney scored last race victory at the Winton 360.
With the Pirtek Enduro Cup of the Wilson Security Sandown 500, the Supercheap Auto Bathurst 1000 and the Armor All Gold Coast 600 just weeks away anywhere up to eight drivers are in sight of the Championship lead.
Whincup leads on 1847 points from Craig Lowndes (1800) and Will Davison (1792). There are just 245 points to ninth placed Garth Tander, well inside the 300 points available at each event.
Following James Moffat's breakthrough win for Norton and Nissan Motorsport yesterday, Pepsi Max Crew FPRs Mark Winterbottom won the middle race today and 17th the second, Whincup failing to finish and 13th with Lowndes 12th and 10th, largely due to poor qualifying.
"We've still got more stuff to come so it's a fantastic time for the Holden Racing Team and it's a great time of year to be coming on strong with Murph (Greg Murphy) on board for Bathurst.
"It's still very open. We have to share a car with someone else which is really exciting but I'm very glad to have Murph and I am sure I will be learning a lot from him at those three events.
"We are in a really strong position."
Whincup's forgettable weekend started yesterday and continued today when he became involved in a first lap stoush from the start line. Whincup got mixed up in an accident that wasn't his, forcing him to pit with major front end damage. He returned to salvage any points he could.
In the first race Whincup was the innocent victim when GRM Fujitsu Holden Commodore VF driver Alex Premat skidded across the infield and back into the pack.
Russell Ingall's Supercheap Auto Commodore was eliminated on the spot, while Whincup pitted four times before retiring his Red Bull Commodore.
"When you start at the back you are vulnerable for first corner incidents and that's exactly what happened," Whincup said.
"I wanted to limp it home to get some points and be classified as a finisher but then the front wishbone broke and I had to pit. It was day over.
"We've lost massive Championship points this weekend and we may be fighting to get the lead back come the enduros."
Winterbottom, who had never won at Winton, launched into the lead at the start in his FPR Pepsi Ford Falcon from third on the grid as pole qualifier Jason Bright and surprise second fastest Ton D'Alberto hesitated.
He established an early gap but several times during the 34-lap sprint race Bright closed on to his rear bumper but could never get close enough to make a lunge in his BOC Commodore.
Courtney finished third after passing D'Alberto in his HiFlex Commodore , who held off Shane van Gisbergen (VIP Commodore) and David Reynolds (The Bottle-O Falcon) to claim fourth.
Yesterday's race winner Moffat qualified a poor 25th, but drove a brilliant race through the field to 11th.
Some reshuffling and tightening of the top 10 in the Championship will make it even more interesting heading into the PIRTEK Enduro Cup - the next V8 Supercars Championship event, the Wilson Security Sandown 500 in Melbourne.