As he did in Paris last week, Van der Burgh claimed victory in the 50m breaststroke final in a winning time of 25.75 secs.
"I'm very satisfied with my performance. The pool is very fast and I'm looking forward to the 100m breaststroke tomorrow," said Van der Burgh.
He had to settle for bronze though in the 200m breaststroke.
His compatriot Chad Le Clos took the 200m butterfly final ahead of Germany's Philip Heintz and China's Hao Yun.