The three-times British Open champion, riding Catwalk IV, won a keenly-contested jump-off involving 11 other pairs.
Belgian Grégory Wathelet on Baloudana and Michel Robert of France riding Nenuphar Jac came in second and third respectively.
Whitaker clocked a time of 38.61 seconds to top the timesheets and claim his first victory of the Grand Prix season.
The versatile rider from Huddersfield's ability to combine speed and caution, coupled with his horse's supreme agility over the jumps, proved too much for the rest of the field.
Others were not so skilled at finding the right balance; Dutchman Henk van de Pol stormed round in 38.73 seconds - fast enough for second place - but he had to settle for 11th in the end, having knocked down two fences.
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