The 30-year-old finished two shots ahead of England's Matthew Baldwin and Spaniard Jorge Campillo, following a four-under-par round of 66, on a significantly shortened Mount Edgecombe CC.
The tournament was reduced to 54-holes after heavy rain made the course unplayable for most of the first three days.
Van der Walt pulled on his golf clothing on Saturday level with Baldwin and Campillo at 11-under-par, three shots behind Daniel Brooks.
Brooks' challenge quickly ended after a disastrous nine holes at the start of his final round that saw him drop back to eight-under.
Entering the back nine on Saturday, van der Walt and Baldwin were tied at 12-under, with Campillo, who started his round with 11 straight pars, a shot further back.
An eagle at the 12th followed by a birdie at the 13th saw van der Walt edge a shot ahead of Baldwin.
The Englishman was unable to find a reply to van der Walt's charge and a further birdie for the South African at the 15th gave him a two-shot cushion that he never relinquished.
It was perhaps fitting that the tournament named after the former South African president, and brought forward by a day to not clash with his funeral, produced a home winner.
"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 for ever," van der Walt said.
Van der Walt, who admitted that he had been struggling with form and injury recently, also topped the co-sanctioning Sunshine Tour Order of Merit following his victory.
"To win the last event of the year is going to make Christmas a lot more fun," he said.
© Copyright Press Association
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