Trained by John Size, Waikuku was held up by jockey Joao Moreira in the early stages of the mile contest but travelled powerfully past rivals coming off the home turn to lock horns with the front-running Beauty Generation in the closing stages.
The pair pulled just over four lengths clear of the rest of the field but Waikuku always looked to have more left and got the better of last year's winner by a neck.
One of Hong Kong's most improved milers, Waikuku registered his first Group 1 victory having previously been denied a maiden top-level success by Admire Mars in the Hong Kong Mile last month.
After reeling off ten successive wins – including five at Group 1 level – the seven-year-old Beauty Generation has now failed to win any of his last four starts.
Another win for Size as Beat The Clock retains crown
Beat The Clock recovered from a slow start out the stalls to successfully defend his crown in the Group 1 Centenary Sprint Cup at Sha Tin, sparking jubilent celebrations from jockey Moreira.
The John Size-trained six-year-old was last of seven as they broke away and had to battle through the pack to put himself back into contention entering the home straight.
Moreria drove Beat The Clock to the lead with 150m left to run and the 6-4 favourite never looked back, staying on well to defeat Thanks Forever by a neck to record his fourth top level success.
Hot King Prawn, who lost out to Beat The Clock by a neck in the Group 1 Hong Kong Sprint last time out, finished one-and-a-half-lengths behind the winner in third.
Size continued a successful day having already recorded a group 1 success on the card, and has now won every renewal of the six-furlong Centenary Sprint Cup, after landing the first edition with D B Pin in 2018.