Whibley's main rival for the GNCC crown, American Kailub Russell, crashed several times and consequently was playing catch-up.
The racing was intense, with Mullins taking the lead, which he held until the finish, with Whibley and DuVall battling behind, until it all turned sour for the Kiwi rider when he ran out of fuel.
Whibley received fuel from another rider on the course and eventually crossed the line in fourth spot, behind Mullins, DuVall and Russell. However, a 15-second time penalty was imposed on Whibley for refuelling outside the designated pit zone, relegating him one position on the track, to fifth, his worst result of the season.
"I'm not sure why I ran out of gas. Lucky for me that (American rider) Jimmy Jarrett had problems and was right there where I rolled to a stop. He found an old beer can and we started ferrying fuel over to my bike. A couple of spectators arrived and lent a hand and I was soon back in the race," Whibley said.
"As we were ready to leave the track, we were called into the promoter's truck and told a protest had been lodged and that a time penalty was being issued and I was also being docked a position. Now the points lead lies in Kailub's hands going into the last round. It will be an exciting race."
Two other Kiwis competing at Indiana, Wellington's Rory Mead and Mokau's Adrian Smith, managed seventh and ninth overall respectively.
Mead had raced a Yamaha YZ450F to win the 2011 New Zealand Enduro Championships before heading off to the US, while Smith clinched both the 2012 national cross-country and enduro crowns - riding a Yamaha YZ250F - before making his American debut just a few weeks ago.
The refuelling disaster may ultimately cost Whibley the GNCC title, but, with one major American title in the bag already for 2012 - the Off-road Motorcycles and ATV (OMA) Championship - the 34-year-old former Manawatu forestry worker, affectionately dubbed "The Axeman" on the US motorcycling scene, is still hoping he can make it two championship wins in the United States this season.
The 13th and final round of the series is set for Loretta Lynn's Hurricane Mills, Tennessee, on November 3 and 4.