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Le Clos finished second in his heat in a time of one minute, 55.23 seconds - the fourth fastest of all the heats in the men's 200 metres butterfly.
The 20-year-old said he was surprised with his performance, coming close to his personal best.
"I'm happy with the time," Le Clos said.
"I'm pretty sure I will make it through to the semi-final, it will be tough and I need to be faster."
It was an otherwise disappointing performance in the pool with Karin Prinsloo crashing out in her heat of the women's 200m freestyle.
Prinsloo finished seventh with a time of 1:59.24 in her Olympic debut and will have another chance to make a splash in the 200m backstroke.
Meanwhile, Kathryn Meaklim's Olympics have come to an end as she failed to progress past the heats of the women's 200m individual medley. Meaklim finished seventh in a time of 2:15.25 to close the curtain on her time in London.
A clinical hat-trick by Australian midfielder Jamie Dwyer helped his team to a 6-0 victory over the South African men's hockey team in their Olympic pool A opener on Monday.
SA conceded two penalty strokes and too many set-pieces as world number one Australia stamped their authority and set the benchmark for the rest of the tournament.
The SA women's rowing pair of Lee-Anne Persse and Naydene Smith missed out on qualifying for the A final, and a chance for a medal, after finishing fifth in the repechage in seven minutes, 18.96 seconds (7:18.96).
Persse and Smith will compete in the B final on Wednesday.
The country's only entrant in archery, Karen Hultzer, was eliminated in the first round of the women's individual event.
Hultzer, who was 46th of 64 competitors in last week's ranking round, won the third set against former European Championships bronze medallist Pia Lionetti, but the South African lost the match 6-2.
In beach volleyball, the men's team of Freedom Chiya and Grant Goldschmidt went down in straight sets, in their second successive group match, to the Latvian pairing of Aleksandrs Samoilovs and Ruslans Sorokins.
Gideon van Zyl was eliminated in the last 32-stage of the men's 73kg discipline by Rustam Orujov of Azerbaijan in four minutes and 34 seconds, bringing an end to his Olympic campaign.
