On Friday, Omanyala had set a time of 9.86 seconds.
Omanyala from Kenya Police beat compatriot Steve Onyango to second place in the third heat in 10.34 as they both qualified for the semi-finals.
In the semis, the African 100 metres record holder clocked 9.95 seconds ahead of South Africa's Henrico Bruintjies who came second in 10.35.
Meanwhile, Japan-based Samuel Kibathi and Rebecca Njeri emerged top in the men's 5,000 metres and women's 10,000m races respectively.