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Le Clos touched in third place in 1:59.45, which was good enough for a spot in the semi-finals while Townsend missed the cut, with his seventh placed 2:00.67, in one of the slower heats.
Suzaan van Biljon finished fourth in her 200m breastroke heat, setting a personal best of two minutes, 25.89 seconds (2:25.89).
Her ninth place standing overall sees her through to the semi-final later in the evening.
Darren Murray third in his 200m backstroke heat, in 2:00.01, but his overall placing was not good enough to make it through to the semis.
Both Van Biljon and Le Clos are in action again in the evening session where they compete in their respective semi-finals.
Meanwhile, the South African rowing duo of Naydene Smith and Lee-Ann Persse put in a strong effort to finish second in the women's pairs B final on Wednesday.
The crossed the line behind China's Yage Zhang and Yulan Gau.
Smith and Persse started well and led the race to the 1000 metre halfway mark but Zhang and Gau dug deep to come back strongly at the end.
Team SA's beach volleyball's pair of Freedom Chiya and Grant Goldschmidt, seeded 21st at the Olympics, are in action against Poland.
With Poland seeded ninth, and the South Africans having lost both of their previous matches by two sets to nil, against the US and Latvia, Wednesday's match will see the end of the South African's Olympic campaign.
