The big Southland rider dominated the final to finish clear of Malaysia's Josiah Ng and van Velthooven, who had won his heat against five Australians.
Archbold, in his first track competition since the London Olympics, was second in the flying lap in 13.499s, third in the points race and won the elimination over compatriot Pieter Bulling (Invercargill), who is part of the BikeNZ endurance track squad based in Europe.
That leaves Archbold clear at the top after three events on six points ahead of Australians Alex Edmondson on eight and Scott Law on 15. Bulling is fifth on 18 points.
Mid-Canterbury cyclist Lauren Ellis and fellow Olympian Jaime Nielsen are in third and fifth respectively in the women's omnium.
Ellis (Hinds) was third in the flying lap and elimination and fourth in the points race to be on 10 points behind Australian Isabelle King who won all three opening day disciplines.
Dunedin's Katie Schofield finished ninth in the women's keirin won by Hong Kong's Wai Sze Lee over Olympic sprint gold medallist Anna Meares.
Today's action features the final three events in the omnium, men's and women's sprint and junior endurance events.