American Mullins headed into the weekend's double-header final with a solid lead over defending champion Josh Strang (Suzuki), of Australia, and 2009 GNCC champion Whibley, but his position became threatened on day one when his engine failed and he rolled to a stop.
Whibley took over the lead with Mullins' KTM teammate Cory Buttrick in second, while Mullins was left frantically trying to restart his bike.
At the end of three hours of intense racing, Whibley took the chequered flag with an 11-second gap over Buttrick. Third place went to Strang, who kept his title hopes alive with the finish.
"I can't control what anybody else does so I just have to go out there and win races," Whibley said.
"Late in the race, I saw Mullins' bike lying beside the track so I knew I had the lead at that point.
"It was tough to make up time in the woods so I was hitting the creeks as hard as I could to try to get it done."
After swapping his engine for a fresh one, Mullins was able to make the final lap and was credited with 14th position, which left the North Carolina rider with an even smaller advantage over Whibley in the standings as they headed into day two.
Mullins put everything beyond doubt with a scintillating win on day two, becoming the first American to win the GNCC title since Rodney Smith held it in 2004.
"The track was really rough," Whibley said.
"But it's good to finish the year where we did, considering the problems we had at the start of the season."
Defending champ Strang was unlucky to run into trouble with tree roots on day two that caused him to crash and break his leg. However, he still wound up third overall in the championship.