This forced a jump off between McNaught-McFarlane and Wilson. McNaught- McFarlane went first and produced another clear round in 52.68s.
When Wilson and her 11-year-old pinto took a brick from the wall on their second jump McNaught-McFarlane had the $40,000 first prize.
"I knew Amanda was green at this level and if I pushed her she will make a mistake. At the same time my horse was tired and that last fence was a bit nerve-wracking," McNaught-McFarlane said.
She will be back at the show again next year.
"This is the show. It has a European feel and it's the show where the money is ... it pays for my year."
She pointed out one of the keys to her success were the numerous bananas she fed to her horse before and during the class.
McNaught-McFarlane was full of praise for Deeg.
"We need designers like you to improve the sport and raise the standard."
Deeg said some may be critical of the fact seven riders went clear in the first round.
"The first round does not have to kill horses and riders to get results. I like to show spectators the beauty of the sport. There were no eliminations and no riders fell down ... there was drama in the jump off and this is what we needed," he added.
Wilson didn't blame the dropped brick on her horse.
"He was incredible out there. That whoopsie wasn't his fault - it was a bit of a miscommunication between us. He is a very extraordinary horse."
It is just their fourth season competing. Wilson bought the horse sight unseen as an eight-year-old off Trade Me. He is called Cassanova for the perfectly shaped heart on his neck.
Canterbury's Steffi Whittaker, riding Ngahiwi Cruise, won the Fiber Fresh Junior Rider of the Year class earlier in the day. Waikato's Drew Carson, who rode Double Shott, was second.
There was hot competition in the dressage arena between Rio hopefuls Julie Brougham of Manawatu aboard Vom Feinsten and Waikato's John Thompson on JHT Antonello.
Brougham had to concede her Dressage Horse of the Year crown to Thompson, riding in his first HOY, but she did set a new Australasian mark for the musical freestyle, bettering her year-old effort from last year's HOY. She also nabbed her last necessary qualifying score that will make her eligible for Rio.
Thompson was chuffed to score two personal best scores.