Mike Gee-Taylor with Alister Bradley also had a good day in Egmont, finishing both fifth overall and fourth in D Class for the round.
But the most prized number is NZ1 and that belonged to Cowper, who finished with 615.5 penalty points, well clear on the day from Counties driver Phillip Walton (680.9) and Auckland's Scott Biggs (744.8).
Even getting a high 80 penalty points on the second to last obstacle did not derail Cowper and co-driver Andrew Bielby's title hopes, as during an overcast day with rain threatening throughout, the pair got the better rub of the draw for going first on certain hill and bog obstacles, before the mud had really been thrown up.
"The big water holes can get harder or easier [through the day]. You just don't know," Cowper said.
"We won the day and that obviously gave us the championship quite easily.
"We were 65 points or so ahead of the next guy and as far as the championship goes, he wasn't a threat.
"We were keeping an eye on the top guys through the day, we knew if we were anywhere near up there [we'd win]."
The other NZ1 contender was Wellington's Phil Conwell, who had Wanganui 4WD's Paul Chapman as his co-driver - and on the day they came second in C Class and seventh overall to finish behind Cowper in the points.
Key to tackling, or surviving, the 30 hill and bog courses is making constant adjustments - such like the amount of tyre pressure - while also quickly adapting when there are problems with the shocks and springs which come from pushing these machines to the limits.
Early in the morning session after one vertical climb, the Harrison's had to quickly take their truck off course for running repairs.
"I think we're sitting at the moment with 120 [points] on the board, but now we're broken. We've got no left steer," said Renee Harrison.
They were soon back on track, while Whanganui's Campbell Huston and Daniel Charlton likewise quickly tended to the rear tyre area of their D Class truck, in the middle of tackling three hillside obstacles in a row at the western boundary of the farm.
"We've broke it [back left tyre mount], but we're ready to go again," said Huston.
At this time, due to the draw, around 4-5 of the Whanganui crews ended up together, which was a good chance for some co-operation and discussion about the best routes to travel up the vertical climbs.
"It's a pretty social sport, you get a chance to have a chat to the guys," said Cowper.
Across the way, Gee-Taylor explained how himself and Bradley were regaining their momentum after struggling at the start.
"It's a game of two halves," Gee-Taylor said.
"The first hazard was not so good, and after that we're on our way.
"It's like anything - they don't come with a guarantee."
Having claimed yet another national crown, Cowper has decided to run a limited schedule for next season's six rounds of the nationals, focusing on just the three events which make up the Central region.
Bielby joined him for the last four rounds this season after original co-driver Lance Brasting broke his shoulder in a non-related accident.
Now Cowper and Bielby will team up in a rally car to run events next year.
But immediately on the horizon is Cowper's own Suzuki Extreme 4x4 Challenge - the invitation event he hosts on the custom-made course at his Turakina farm - on April 10.
Last year's inaugural event saw some of the country's top 15 drivers invited to compete in the one-off championship, much like an 'All-Stars' format.
"All these top guys will pretty much be coming down. They've got two weeks to get their trucks sorted," said Cowper.
The event will again be filmed for TV3's CRC Motorsport show.