The South African was desperately trying to conserve energy as he bids for a 200/400m double but was forced to go deeper than he would have liked by Botswana's Baboloki Thebe in the second of three semi-finals, eventually clocking 44.22 seconds.
By that stage two 21-year-olds had fired out a warning with massive personal bests.
Steven Gardiner improved his own Bahamas national record and went under 44 seconds for the first time, clocking a 43.89 which he might pay for in the final on Tuesday.
Nathon Allen also set a Jamaican record, taking almost half a second off his best with 44.19.
Botswana's Isaac Makwala looked very comfortable in winning his heat in 44.22 seconds.
Van Niekerk was originally drawn in the opening heat but organisers changed the lineup, which pleased the South African.
"Whoever changed it, thank you, I wasn’t ready for 43 seconds,” he said.
"It seems like every time we go on the track someone breaks 44 seconds. It is good competition but it just means I always have to be on my game.
"I'm just trying to get through the rounds as conservatively as I can."
American's big hope Fred Kerley scraped into the final as a fast loser but former Olympic and world champion LaShawn Merritt, another man to serve a doping ban though unlike compatriot Justin Gatlin loudly cheered by the London crowd, failed to make it.
(Editing by Ed Osmond)
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