He defeated American BeeJay Lee by 0.33 seconds.
"It was challenging," Van Niekerk told reporters. "To be honest I thought I did a 400. It was a bit tough."
The Olympic 400m champion was tuning up to run both the 200 and 400 at August's world championships in London.
"I've still got a lot of work to do and have a lot of areas I need to look into," he said. "But it was a positive win for me today.
Bahamian Olympic women's 400m gold medallist Miller-Uibo wiped out American Allyson Felix's 200m straightaway world best with another runaway victory.
She finished in 21.76 seconds in taking out Felix's 2010 best of 22.55 seconds at the Manchester, England, street meet.
Typically, 200m races are run around a bend and only those are recognised as world records. Jamaica's Usain Bolt has the men's record of 19.19 seconds and American Florence Griffith Joyner holds the women's mark at 21.34.
Bowie, a double sprint medallist at Rio, took down another Felix world best in the women's 150m straightaway, running 16.30 seconds.
Felix set the previous best of 16.36 at Manchester in 2013.
London Olympic champion Jenn Suhr was upset in the women's pole vault by Canadian Alysha Newman, who cleared 4.60 metres.
Suhr claimed second with a vault of 4.50.
(Reporting by Gene Cherry in Raleigh, North Carolina; Editing by Ian Ransom)
