Monster Energy/Pro Circuit/Kawasaki's Brett Metcalfe rounded out the podium for the second moto and took third overall after a fifth place performance in moto one.
Villopoto worked through traffic in the opening portion of the moto again, taking the lead on lap three to maintain his undefeated record at Budds Creek and notch his third straight overall victory at the facility.
"I've been able to ride good here the last three years," said Villopoto. "I like the track. I like going the other way a little better, but it turned out decent. I didn't get the start I wanted in both motos so I just had to put my head down, get around the guys, and pull the gap. I don't want to put myself into a position to get taken out. I just take my time, look for some lines, and work around guys. The lap time was kind of short today, which makes it harder because it becomes more mental."
Stewart currently holds a 105-point lead over team-mate Ferry in the AMA Motocross standings. In AMA Motocross Lites, Villopoto has a 103-point advantage over Dungey.