Makwala, who is also scheduled to race in the 400m final on Tuesday, pulled out due to a medical condition, organisers said.
Even before the Botswana's withdrawal there was a somewhat subdued atmosphere surrounding the event after Usain Bolt, winner of the last four world and three Olympic titles, had decided before the championships not to take part.
The Jamaican opted to run only in the 100 metres and the 4x100 relay in London, his last competitive appearance.
Meanwhile, Canada's Andre de Grasse, another favourite, is out for the rest of the season with injury.
South African Wayde van Niekerk, who ia aiming for a 200/400 double, comfortably won his heat in 20.16 seconds, easing up as he reached the line to finish neck-and-neck with Briton Daniel Talbot, who ran a personal best.
Officially, Van Niekerk won by one millisecond.
Nineteen-year-old Sydney Siame set a Zambian record as he won his heat in 20.29.
"I have been preparing for this for so long," he said. "At the last world championships I was eliminated in the first round. I've experienced the rounds but I want to be in the top eight."
Jamaican Yohan Blake, whose career has been plagued by injuries since he won two sprint silvers at the 2012 London Olympics, also progressed, winning his heat in 20.39.
Weir, runner-up to Bolt at the worlds in Moscow four years ago, missed out after finishing fourth in his heat in 20.60, not good enough to take him through as one of the fastest losers.
Trinidad's Jereem Richards ran the fastest time of 20.05.
(Reporting by Brian Homewood; editing by Ken Ferris)
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