Le Clos got off to a poor start and was well out of the medal placings at the turn as Steffen Deibler stormed into the lead Saturday.
At close, Le Clos looked out of contention before producing three massive strokes in the last 20m, which saw him surge into first place as he touched home ahead of Laszlo Cech and Konrad Czerniak.
American Ryan Lochte, who had been the fastest in qualifying, could only finish sixth.
Le Clos was delighted that he had followed the 200m butterfly title he won earlier in the week with the 100m crown.
“I’m very happy, I wanted the double for a long time and now I have got it. I feel good now. I was a bit worried about my fitness as I came here but everything has come good in time,” said the delighted South African.