Rees' elder brother and teammate Mitch Rees, on an identical Honda CRB1000SP1, was in second spot and managed to keep Hoogenboezem honest until he crashed spectacularly on the seventh lap of 10. His bike wrecked, he was unable to continue the race.
Meanwhile, Damon mounted a thrilling comeback, picking off rider after rider until he finally slotted into third spot, just behind Hoogenboezem's teammate Jake Lewis, of Canterbury, as the riders crossed the finish line.
Rees redeemed himself in the two Superbikes races that followed on Sunday, winning both and taking the overall win for the class, although this has been declared provisional as engine checks are yet to be undertaken on several machines.
"I could not have asked for a better weekend actually. It was not perfect, but pretty damn close. I made the best of a bad situation," Rees said.
"Some would say I should be happy with my third on Saturday, but I'm never happy unless I'm winning. "I'm obviously happy to come away with my second GP title win too, my second after winning it on a 600 bike in the past.
"Winning the GP title was the one I really wanted because I'm not here in New Zealand for the full series. I head to the United Kingdom after round two here.
"The momentum just has to keep building. We are going to do some testing in Timaru on Wednesday and hopefully I can be here in the same spot on the top of the podium next weekend too."
Coupled with his bonus point for qualifying fastest, Rees now enjoys a two-point advantage over Hoogenboezem as the series heads to Timaru for round two this weekend.
His charge from last place to third in Saturday's first race also gave Rees a new Ruapuna lap record of 1m, 29.189secs, beating the mark set 10 years ago by the now-retired Andrew Stroud.
Mitch Rees also crashed in the first of Sunday's two Superbike races, but bounced back to finish seventh in the last outing.
Other class leaders after the weekend's racing are Whanganui's Richie Dibben (Supersport 600); Whangarei's Jason Hearn (Supersport 300); Whangamata's Benjamin Rosendaal (650 Pro Twins); Christchurch's Dennis Charlett (250 Production, support); Christchurch's Matthew Hoogenboezem (Supersport Lightweight, support); Auckland's Peter Goodwin and Kendal Dunlop (Sidecars); Invercargill's Cormac Buchanan (Supersport 150) and Nelson's Tyrone Kuipers (GIXXER Cup 150, support).
2020 New Zealand Superbike Championships schedule
Round 1: January 11-12, Mike Pero Motorsport Park, Christchurch.
Round 2: January 18-19, Levels International Raceway, Timaru.
Round 3: March 7-8, Hampton Downs Motorsport Park, North Waikato, Mike Pero MotoFest.
Round 4: March 28-29, Circuit Chris Amon, Manfeild, Feilding.
Round 5: April 4-5, Bruce McLaren Motorsport Park, Taupō.
