Ndiku, the world indoor 3000m champion, made the most of the absence of injury-hit Olympic champion Farah to win the first gold medal on offer at the Hampden Park track.
With his hair dyed gold in expectation of victory, Ndiku triumphed in 13min 12.07sec over the 5km race with teammate Isiah Koech claiming silver in 13:14.06, with New Zealander Zane Robertson claiming bronze (13:16.52).
"I could see it wasn't going to be easy. There was a lot of tough competition and I needed to know when to attack," said the champion.
Australian Michael Shelley prevented a Kenyan marathon sweep by producing a stunning final 8km to win gold with Kenya's Stephen Chemlany in second and Uganda's Abraham Kiplimo taking bronze.
In the blue riband 100m, Nickel Ashmeade, part of the gold medal-winning Jamaican 4x100m relay team from the Moscow worlds last year, clocked 10.40 seconds to win his heat.
The weight of the Caribbean island's expectations are resting squarely on Ashmeade's shoulders in the absence of Bolt, who will compete solely in the relay in Glasgow after an injury-plagued season.
Trinidad and Tobago's Richard Thompson, the 2008 Olympic silver medallist, could only finish third in his heat.
In the women's 100m heats, it also wasn't all plain sailing for Thompson's teammate Michelle-Lee Ahye, who rebounded from a sluggish start to come in second in her heat in 11.44 behind Canadian winner Khamica Bingham.
Jamaica's Veronica Campbell-Brown looked slick in winning in 11.29sec and she will be joined in the semi-finals by teammates Schillonie Calvert, who clocked the same time in nailing her heat, and Olympic silver medalist Kerron Stewart (11.35).
On the final day of track cycling, Stephanie Morton took gold for Australia in the women's sprint seeing off compatriot and reigning champion Anna Meares.
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