Manawatu's Whibley, a two-time former cross country champion in the United States, had to settle for overall runner-up, while Raglan's Brandon Given, Glen Murray's Sam "Charlie" Brown and Whanganui's Seth Reardon rounded out the top five seniors for 2021.
Meanwhile, Taupo's Wil Yeoman dominated the 90-minute junior grade races on both days at the weekend and the 15-year-old therefore easily wrapped up the junior crown for 2021.
Runner-up junior rider for the series was Eketahuna's Luke Brown, with Cambridge's Bailey Morgan, Rotorua's Daniel Bates and Katikati's Ryan Morrissey rounding out the top five.
Masterton's Max Williams was the best of the 85cc bike riders this season, impressive in finishing eighth overall in the junior grade.
"It was quite tight and technical terrain on Saturday, but a faster, more free-flowing course on Sunday," said Motorcycling New Zealand cross-country commissioner Chris Smyth.
"There was forestry, bush, open farmland paddocks ... a bit of everything really. Everyone seemed to enjoy both tracks and days in the South Island.
"The double-header format seemed popular with the riders too and we may look at doing more of that next season."