He took silver in the 100-metre breaststroke event on Monday.
The 25-year-old, who last year won the Olympic gold over the same distance and is also world record holder, was beaten by Australian Christian Sprenger.
Van der Burgh finished in a time of 58.97 – 0.18 slower than Sprenger. Bronze went to Brazilian Felipe Lima.
Van der Burgh previously won gold in the 50m breaststroke at the 2009 world championships, bronze over the 50m and 100m breaststroke at the 2011 worlds, as well as the gold in London.
The defending champion, Norway's Alexander Dale Oen, died in Arizona in 2012 during a training camp of a heart attack. – Sapa