The British rider had not topped the podium since he won the Spruce Meadows CSI5* in Calgary last year but he got back to winning ways after edging out Laura Kraut in Spain.
Whitaker, who came third overall in last season’s GCT, opted for caution over speed and delivered three clear rounds with his chestnut gelding Viking.
In the final round the 53-year-old Olympian was over five seconds slower than Kraut, who was riding Pénélope Leprévost’s former mare Jubilée d'Ouilly, but the American had a fence down which forced her down into second place.
“He (Viking) is always knocking on the door of the big wins, so it is the first time he has won,” said Whitaker. “It’s good for me and it is good for the horse as well.”
Brazilian Alvaro de Miranda with AD Rahmannshof's Bogeno completed the top three.
The GCT next heads to Hamburg on May 9.