The 29-year-old Yorkshireman claimed a £38,000 top prize after producing a superb performance on Utamaro D Ecaussines.
It was Whitaker’s third World Cup win, but his first on British soil, as he triumphed ahead of Belgium’s Karel Cox in second and American Laura Kraut, with his uncle Michael Whitaker finishing fourth aboard Valmy de la Lande.
“I’ve been coming here since I was two or three, and have many memories,” William Whitaker said.
“This is what makes you get out of bed. In fact, it feels a bit surreal.
“I knew I had done a good round, but when you looked at the quality of riders to come after me, I wasn’t confident.
“But it all worked out as I planned.
“It helps to be on a horse like him – he’s got such a good brain.
“I was struggling to get him into canter in the warm-up, but when he gets into the arena he lights up.
“This is by far the best win of my career.”
A total of 18 combinations from 37 starters made the jump-off, including five British riders, but it was Whitaker who triumphed in a time of 37.02 seconds, with Cox 19 hundredths of a second behind on Evert, and Kraut completing the podium places aboard Zeremonie.
Sir AP McCoy secured victory for the second year in succession in the Markel Champions Challenge at the Olympia Horse Show in London.
The 20-time champion jockey, 44, was part of a relay team, which also included Ryan Moore, coached by Nick Skelton for the showjumping event in aid of the Injured Jockeys Fund.