However, Ashburn had strife when he failed to brake at a slick corner and took a fall, which left the Tennessee native at the back of the field.
Whibley continued to force the pace but it was American Kailub Russell who gradually took control of the three-hour race for what was his second straight victory of the season.
Australian Josh Strang was second, with Americans Charlie Mullins and Chris Bach third and fourth and Whibley a plucky fifth. Just behind him was Ashburn, who did well to get that close, while Wellington's Rory Mead was 10th.
The weekend's result left Whibley fifth in the GNCC national standings overall, level with American rider Thad DuVall but a vast 78 points behind series leader Mullins. The next race will be at Snowshoe, West Virginia, on June 30.
Whibley is fourth overall in the parallel OMA series, just 15 points behind leader Russell Bobbitt.