Van Niekerk is on fire this season, having run personal bests in the 100m (9.94sec) and 200m (19.84) last month, and setting a new world best time of 30.81sec in the rarely-run 300m in Ostrava last week.
That time beat a long-time record held by Michael Johnson, the legendary US athlete whose record in the one-lap race he also beat when winning gold in Rio.
The 24-year-old timed a world lead of 43.62sec in Lausanne, well ahead of second-placed Botswana's Baboloki Thebe.
Van Niekerk has only run the 400m faster on two occasions: when he won his world title in Beijing in 2015; the other was a year later when he won Olympic gold.
Hailed by eight-time Olympic champion Usain Bolt as his successor as leader of the sprinting world, with the Jamaican legend due to retire after the world championships in London in August, Van Niekerk said he was constantly inspired by his performances.
"I didn't come with a specific time in mind but I am pleased with this result," he said.
"I do have a love-hate relationship with the 400m, but I always try to approach it with a positive mindset, not setting myself any limits.
"And the performances keep me going along, which keeps me passionate about what I do."
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