Le Clos came third in his semi-final clocking 50.73 seconds behind Thomas Shields (USA) and Ryan Lochte (USA) on Wednesday.
The final will take place on Thursday.
South Africans Devon Myles Brown (1:44.89) and Leith Shankland (1:44.91) narrowly missed out on a place in the men's 200m freestyle final, while Jessica Pengelly (4:37.66) also came up just short of a place in the final of the women's 400m individual medley.
It was a similar result for the women's 4x200m freestyle team of Karin Prinsloo, Michelle Weber, Kyna Pereira and Jessica Pengelly who placed on the reserve list for the finals in a time of 8:02.49, well off their qualifying time of 8:55.99.
In the men's 100m breaststroke Giulio Zorzi missed out on a place in the semi-final place in a time of 59.09. – Sapa