Kiprotich was the surprise winner at last year's London Games but started as one of the favourites in Moscow and became the first non-Kenyan to win the title since 2005.
Ethiopia's Boston marathon winner Lelisa Desisa was second in 2:10:12 and compatriot Tadese Tola took third a further 11 seconds back on a warm sunny day in the Russian capital.
Part of a large leading pack for most of the race on a course which included three 10km loops along the Moskva river turning at the iconic Red Square, Kiprotich began pushing the pace just after the 30-km mark and the group slowly started to break up.
With just over two kilometres to go, the battle for gold was between Kiprotich and Desisa and the Ugandan finally broke his rival as they ran through the Olympic Park and entered the stadium alone, waving to the crowd.
Kiprotich had a quick look back across the bright blue track when a cheer went up as Desisa entered the stadium but there was half a lap between them and the Ugandan ran through the finishing tape with his arms in the air and a smile on his face before bowing to the crowd.
"I realised I could win after 40km. Then I just kept pushing. I decided to break off but my competitors were strong and I had to apply some tactics," the 24-year-old told reporters.
"I prepared for the race really well. It is fantastic that I actually train together with six of my competitors, said Kiprotich who is coached by Kenya's 1992 Olympic steeplechase silver medallist Patrick Sang in Eldoret.
It was Uganda's second ever world championship gold after Dorcus Inzikuru won the women's 3,000 steeplechase in 2005.
Peter Some in ninth was the first Kenyan finisher for a team that was missing twice world champion Abel Kirui through injury.
(Editing by Justin Palmer and Pritha Sarkar)
