Le Clos bettered his own record, set in Friday's semi-final, by 0.25secs to a time of 21.95sec.
Sanchez finished second behind Le Clos in a time of 22.08sec.
Results from the fourth day of the 2014 world short course championships in Doha on Saturday:
Men
4x50m freestyle relay
1. Russia 1:22.60 - world record
2. United States 1:23.47
3. Italy 1:24.56
50m backstroke
1. Florent Manaudou (FRA) 22.22 - world record
2. Eugene Godsoe (USA) 23.05
3. Stanislav Donets (RUS) 23.10
50m butterfly
1. Chad Le Clos (RSA) 21.95
2. Nicholas Santos (BRA) 22.08
3. Andrii Govorov (UKR) 22.49
Women
100m breaststroke
1. Alia Atkinson (JAM) 1:02.36
2. Ruta Meilutyte (LTU) 1:02.46
3. Moniek Nijhuis (NED) 1:04.03
200m individual medley
1. Katinka Hosszu (HUN) 2:01.86 - world record
2. Siobhan-Marie O'Connor (GBR) 2:05.87
3. Melanie Margalis (HUN) 2:06.8
Mixed
4x50m freestyle relay
1. United States 1:28.57 - world record
2. Russia 1:29.13
3. Brazil 1:29.17