Eleven riders went clear in the first round, only Olympian Katie Laurie achieving the feat on two mounts, Carlotta and Dunstan Springfield.
Cubitt was the third into the ring and the first to go clear, setting a blistering pace and clocking a time of 42.91s for the shortened jump-off course.
She faced a nervous wait, with three riders then going clear, but none bettering her time. Laurie was closest with 44.07 riding Horse of the Year Champion Dunstan Springfield.
"I knew at the end that it was probably enough - he was very quick and I was confident ... but you never know," said Cubitt.
It was the third time in four years the combination had tasted success at the winery, the Tauranga-bred horse Cubitt has had since he was three, missing last year's event.
"I'm very, very happy, it's always good to come to such an incredible venue - it's very special.
"It's an interesting concept. It's different to a showground where [the horses] have been before - the trucks are parked a bit closer together and the practice ring is smaller than they are used to - they know something a bit different is happening."
The showjumping now moves to Tauranga Racecourse for three days of events while Cubitt turns her attention to the Bayleys Grand Prix on Sunday.
Tauranga rider Sam Morrison, 20, was experiencing the Mills Reef atmosphere for just the second time, riding Biarritz. "It's a lot spookier and there's a lot more [for the horse] to look at - the jumps are quite spooky," she said.
"But it's a good environment - more like it is in England."
Morrison is to accompany Laurie to the United States in April, where Laurie will ride Dunstan Kiwi Iron Mark in the FEI World Cup, also taking secondary mount Frangipanne de Toxandria.
Mills Reef Classic: Lisa Cubitt, Bates Amaretto 42.91s, 1; Katie Laurie, Dunstan Springfield 44.07s, 2; Olivia Robertson Ngahiwi Cisco 48.11s, 3; Rose Alfeld, My Super Nova 48.86s, 4; Mathew Gilmour, Cuba D Esqueimes Z 45.55s, 4 penalties, 5.
