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The Blade Runner, who made history when he set his second fastest time in the heats of his first global able-bodied competition, started slowly in the penultimate round and never recovered, trailing home in 46.19 seconds.
South Africa, however, shone after a slow first two days, with Ruben Ramolefi improving his national record in the men's 3 000m steeplechase.
Ramolefi finished second in his heat in 8:11.50, qualifying comfortably for the final, and improved his national best, set a little over a year ago in Monaco, by 0.13 seconds.
Defending champion Ezekiel Kemboi of Kenya was fastest of the qualifiers, holding off the South African to win the heat in 8:10.93.
“I told myself just to run comfortably and be rhythmic,” said Ramolefi, who controlled the race from the start.
“I didn't try to be technical about it, I just trusted my body.
“On the big screen I saw that we were quite a group, so I thought that I needed to spread the group to leave us less work at the end.”
Ramolefi, 33, is the eighth fastest this year of the 15 athletes in Thursday afternoon's final.
Former national champion Cornel Fredericks and SA record holder LJ van Zyl were both in good form in the heats of the men's 400m hurdles, qualifying comfortably for Tuesday's semi-finals.
Fredericks, 21, finished second in the fastest of five heats, but was given the same time - 48.52 seconds - as Great Britain's David Greene.
“It was a good race. I did everything correctly, and hopefully I can do better tomorrow,” Fredericks said.
Van Zyl, the fastest in the world this year, won a tough heat in 48.58 to beat a field which included former Olympic gold medallist Felix Sanchez of the Dominican Republic and defending champion Kerron Clement of the United States.
“I'm happy to be through because I was a bit nervous,” Van Zyl said.
“The first round was just to break the ice and I'm pleased to be in the semi-finals.”
Wenda Theron, meanwhile, set a personal best in the heats of the women's 400m hurdles, clocking 56.13 as the 17th fastest of the 24 qualifiers for Tuesday's semi-finals.
“I didn't expect anything. I came here to run my heat as if it was my final,” Theron said.
“I didn't expect to be in the semi, and now I am. That's two goals achieved.”
