The world indoor champion held off competition from compatriot Isiah Koech and New Zealand's Zane Robertson to win in 13 minutes, 12.07 seconds.
With Olympic champion Mo Farah absent due to illness, Robertson and brother Jake led the early running before the Kenyans took charge - Ndiku finishing almost two seconds clear of Koech.
England's Fran Halsall became the first woman to complete a Commonwealth sprint double in the pool, adding the 50m butterfly title to her freestyle crown over the same distance by finishing 0.33secs clear of Arianna Vanderpool Wallace.
A Games record time of 2:07.24 gave Belinda Hocking 200m backstroke gold, before compatriot James Magnussen earned another success for Australia in the 100m freestyle.
England's Siobhan O'Connor added 200m individual medley gold to the three bronze medals and one silver she had already claimed at the Games, while Ben Treffers headed an Australian one-two in the 50m backstroke ahead of Mitch Larkin.
Sophie Pascoe of New Zealand took gold in the final of the 100m breastroke SB9 contest, and Australia capped off an impressive day with victory in the 4x200m freestyle relay.
There was an Australian top two in the cycling sprint finals as Stephanie Morton finished clear of Olympic gold medallist Anna Mears, with England's Jess Varnish taking bronze.
Laura Trott's final sprint in the 25km points race saw her edge Wales' Elinor Barker into second, after the pair had finished level, with Matthew Glaetzer topping the podium in the men's keirin event.
It was a close-run affair but the Australian held off New Zealand's Sam Webster, whose fellow Kiwi Shane Archbold went one better to take 20km scratch gold.
Michael Shelley and Flomena Cheyech Daniel clinched marathon gold earlier in the day with the former - a silver medallist in the Delhi Games four years ago - coming home in two hours, 11 minutes and 15 seconds.
There was a big shock in the rugby sevens at Ibrox as reigning champions New Zealand were beaten by South Africa.
The Kiwis have won gold at the last four Games but came up short in a 17-12 defeat after Australia had been dominant in picking up bronze against Samoa.
In the women's fours lawn bowls, South Africa recovered from 9-4 down after nine ends against Malaysia to eventually prevail 14-9.
New Zealand's Jo Edwards saw off defending Commonwealth champion Natalie Melmore 21-15 in the women's singles.
The women's section of the 63kg Group A weightlfting was won by Olauwatoyin Adesanmi with a total weight of 207kg, while India's Sathish Sivalingam lifted 328kg on his way to gold in the men's 77kg contest.