The Olympic champion, who fell on the horse during Wednesday's team final, looked in complete control as he finished with 15.500 points in the final - beating second-placed Lee Chih-kai of Taiwan by a slim margin of 0.067 of a point.
After finishing second in Doha last year, Whitlock regained his world title to match his feats of 2015 and 2017.
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Rhys McClenaghan, who beat Whitlock to win at the Commonwealth Games last year, became the first-ever Irish gymnast to clinch a world medal by claiming bronze.
The 20-year-old McClenaghan earned 15.400.
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