South Africa won the second Test by 7 wickets to level series 1-1.
Play was possible in the last session of the day only after rain washed first and second session.
Captain Dean Elgar scored unbeaten match-winning 96 to help his side chase down 240.
Mohammed Shami scalped Van der Dussen on day 4, the only wicket to fell.
This is South Africa's first Test win at the wanderers vs India