Van Niekerk, who also set the world record when winning Olympic gold in Rio last year, switched off with 10 metres to run to clock 44.22 seconds to win his heat ahead of Botswana's Baboloki Thebe.
Thebe's older teammate Isaac Makwala, like Van Niekerk going for a 200/400m double, won his semi-final easily in 44.30 seconds.
The fastest time was a blistering 43.89sec by Steven Gardiner, a national record for Bahamas.
Nathon Allen was sucked along on his coattails in 44.19, with another Jamaican, Demish Gaye, also qualifying for Tuesday's final with a personal best of 44.55.
Rounding out the eight-man showdown will be American college runner Fred Kerley and Sudanese-born Qatari Abdalelah Haroun.
"Every time we get on the track it seems as though we go to break 44 seconds," acknowledged Van Niekerk.
"It is good competition but it just means I always have to be on my game."
Much is expected of Van Niekerk, the world and Olympic champion who smashed American Michael Johnson's world 400m record when winning in Rio last summer in 43.03.
Even Usain Bolt has pegged the 25-year-old South African as his most likely successor as the athlete capable of dominating the track after the Jamaican sprint star's exit from athletics after these world champs.
Should Van Niekerk, or Makwala, bag the double, it would be the first since Johnson achieved the feat at the 1995 worlds in Gothenburg and a year later at the Atlanta Olympics.
The final of the men's 400m final takes place on Tuesday (22:50 SA time) with the possibility of gold for South Africa.