Medical sources said: “His vital signs were unstable and he had to be transferred [to hospital] for better control and treatment.”
Van Niekerk was discharged from hospital shortly before 11.45pm local time.
The South African’s prodigious effort was more than matched on the day by a winning javelin throw of 92.72 metres from Kenya’s Julius Yego, the best thrown since the Czech Republic's Jan Zelezny won the same title in Edmonton in 2001 with 92.80.
Van Niekerk, meanwhile, went fourth on the all-time lists behind Jeremy Wariner with 43.45, Butch Reynolds 43.29 and world record holder Michael Johnson, who clocked 43.18 in winning this title at Seville in 1999.
The 26-year-old Kenyan - who already headed this year’s world lists with 91.39m - is only 5ft 9in, but he walked tall as he left the throwing area, beating his chest in excitement.
“I’m so happy, I can’t even express it,” Yego said.
After winning the Commonwealth title in Glasgow last year, this was another significant step up for the man from the Nandi district of Tinderet - and a timely one, given the unfortunate news that two female Kenyan athletes, 400m runner Joyce Zakary and 400m hurdler Francisca Koki Manunga, had tested positive for banned performance-enhancing drugs.
Behind Yego, Egypt’s Ihab Abdelrahman El Sayed also made a breakthrough as he took silver with 88.99m, with bronze going to Finland's 2007 world champion Tero Pitkamaki with 87.64.
Defending 400m champion LaShawn Merritt of the United States produced a personal best of 43.65 in second place, with Olympic champion Kirani James of Grenada third in a season’s best of 43.78.
“A PR (personal record), and I just get to take the silver,” mused Merritt, while James commented: “This was one of the toughest races of my life.
"With guys running such times, the world record could be under threat.”
A national record of 44.11 by Olympic silver medallist Luguelin Santos of the Dominican Republic was only enough for fourth place.
That is what you call a classy final…
There was more electric action in the field as Cuba’s Yarisely Silva, who took a pole vault medal to match her name at the London 2012 Games, earned her first global outdoor title with a third-time clearance at 4.90m in a hugely competitive final which saw her accompanied to that point by Brazil’s 2011 world champion Fabiana Murer, eventual silver medallist with a South American record of 4.85m, and Nikoleta Kyriakopoulou of Greece.
Silva’s final clearance provoked scenes of burly joy among her watching coaches and supporters, who included the recently elected IAAF vice-president Alberto Juantorena.
The three finishers in the women’s 3,000m steeplechase raced almost shoulder to shoulder within the final 30m before Kenya's Hyvin Kiyeng Jepkemoi prevailed to take gold in 9min 19.11sec, with Habiba Ghribi of Tunisia, who stuttered over the final hurdle but then accelerated back into contention, earning silver by just a hundredth of a second ahead of Germay’s Gesa Krause, 9:19.24 to 9:19.25.
Zuzana Hejnova of the Czech Republic produced a dominant defence of her 400m hurdles title, finishing almost half a second clear of the opposition in 53.50, the fastest time run so far this year.
Silver and bronze went respectively to US runners Shamier Little in 53.94 and Cassandra Tate 54.02.
August 2015: Two female Kenyans suspended in Beijing after positive doping tests
August 2015: Greg Rutherford completes medal set as Wang wows Bird’s Nest with historic bronze
August 2015: Fraser-Pryce matches Bolt’s golden Bird’s Nest return over 100m
August 2015: Nick Butler: Usain Bolt - saviour of athletics or just a great champion?
August 2015: Bolt bests Gatlin to retain world 100m title in his "hardest race