The 30-year-old finished the shortened tournament on 15 under par to finish ahead of Englishman Matthew Baldwin and Spaniard Jorge Campillo as he picked up his second European title at the saturated Mount Edgecombe golf club.
The win comes on the eve of Mandela's funeral after the former president passed away at the age of 95 last week.
"It's obviously really special, making you part of history," Van der Walt said following his victory which follows his maiden European win last March at the Tshwane Open, also in South Africa.
"Winning the Nelson Mandela at this time, when it's sad for everyone, everyone is mourning and tomorrow's (Sunday) the big day, it means a lot and it's something I can keep close to my heart for ever.
"I haven't been in that good form, I've been struggling with an injury, so this is almost overwhelming. To win the last event of the year is going to make Christmas a lot more fun," he added.
Frenchman Romain Wattel was alone in fourth three shots back, while South African Oliver Bekker was a further stroke back to complete the top five.
Overnight leader Daniel Brooks of England blew a three-shot lead as he ballooned to a six-over score of 76 to slide down the leaderboard and a joint 11th-place finish.
The tournament was reduced to 54 holes after heavy rain washed out the first day's play as the European Tour remains in South Africa and heads to the Durban Open which begins next Thursday.