Van der Walt achieved his win just a day before former South African president Mandela, who died last week aged 95, is laid to rest.
"It's obviously really special, making you a part of history," Van der Walt said.
"Winning The Nelson Mandela at this time, when it's sad for everyone, everyone is mourning and tomorrow's the big day, it means a lot and it's something I can keep close to my heart forever."
Van der Walt carded four under par 66 on Saturday at the tournament reduced to 54 holes due to bad weather earlier in the week. The event also concluded a day earlier than usual so that it avoided clashing with Mandela's funeral.
Van der Walt finished ahead of Spain's Jorge Campillo and England's Matthew Baldwin, who both carded two under par 68s.
Daniel Brooks relinquished his overnight lead following an abysmal start and struggled to a six over par 76 finish.
Having not dropped a shot in his opening two rounds, Brooks succumbed to four bogies and a double bogie in his front nine on Saturday to slide down the leaderboard.
Saturday's win was a welcome return to form for Van der Walt, who claimed his second win on the European Tour this year following his success at the Tshwane Open.
"I haven't been in that good form, I had an injury and have been struggling, so this is almost overwhelming. It almost felt like I have been at the top of my game and then hit rock bottom this year, so to win the last event of the year will make Christmas a lot more fun," he said.
(Reporting by Nick Said in Cape Town; editing by Pritha Sarkar)