Ndiku, 21, the world indoor 3,000m champion, took advantage of Olympic and world champion Mo Farah's absence to produce a performance to match his golden hair.
He won a pulsating final in 13 minutes, 12.07 seconds on a drizzly night at Hampden Park.
Compatriot Isiah Koech took silver in 13:14.06 as the Kenyan pair overtook New Zealand twins Jake and Zane Robertson, who had led for much of the race.
Zane took the bronze in 13:16.52, a season's best.
Farah, who won the 5,000m and 10,000m titles at the London 2012 Olympics and the world championships in Moscow last year, withdrew from the Games last week due to illness.
(Reporting by Sam Holden, editing by Tony Goodson)
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