Le Clos finished in a time of 1:41.45sec, 0.22secs ahead of Russia's Danila Izotov, with America's Ryan Lochte finishing in third in a time of 1:42.09sec.
In other action, Cameron van der Burgh qualified as the fifth fastest for Thursday's 100m men's breaststroke final after finishing fourth in his semi-final in a time of 57.18sec.
Meanwhile, Mireia Belmonte set a new 200m women's butterfly world record.
The Spaniard posted a time of 1:59.61sec to claim the world title, taking 1.17secs off the previous best set by China's Liu Zige in the era of performance-enhancing suits in 2009.
All eyes had been on Hungary's Katinka Hosszu who had been ominous in the heats and the 'Iron Lady' appeared on course for a first title of the meet and possible world record.
With 50m to go Hosszu was 0.89secs under world record pace but Belmonte produced a perfectly judged final two lengths.
Le Clos then took to the pool once more for the 100m men's butterfly semi-final and never looked like being usurped as he blasted his way into the final as the fastest qualifier in a time of 49.25secs, nearly 0.5 secs faster than his nearest competitor.