"It's amazing – when it rained we thought we didn't have a show," JJ Rayner said.
"It was a great ride by Johnathan."
The gelding dug deep in the final stages to keep the challenge of Packing Eagle at bay with the longshot Brilliant Shine taking third money ahead of Ronchi.
Last season, Start Wondering finished runner-up in the Group 1 Haunui Farm WFA Classic (1600m) after his Te Rapa success and he is again likely to head to the Otaki feature.
The disappointment of Saturday's race was the warm favourite Kawi, who was gunning for the eighth Group One victory of his career.
However, he was on the back foot early after he missed the start before he picked up ground 600m from home.
The son of Savabeel was widest into the straight, but he was never a threat in the run home and finished sixth.
Start Wondering is current Whanganui Horse of the Year and reigning NZ Sprinter of the Year.
He was bred in Whanganui by Ian Hadfield and is owned by Stephen and Jo Gudsell - owners of Ag Challenge. – NZ Racing Desk.