The event was returning to the European Tour International Schedule after taking a season off while extensive changes were made to the stunning Leopard Creek Country Club on the edge of the Kruger National Park.
High winds and fast greens made for a testing day and South African Bekker was the man to best conquer the conditions, moving to six under and opening up a one-shot lead over Australian Dimitrios Papadatos.
Frenchman Raphaël Jacquelin was then at four under, a shot clear of a group of nine players including defending champion Brandon Stone.
Bekker - an eight-time visitor to the Qualifying School - finished in the top ten at the Afrasia Bank Mauritius Open at Anahita last time out to seal his fourth European Tour top ten in 67 appearances.
He finished 61st on last season's Challenge Tour Rankings but has eight wins on the Sunshine Tour and made just a single bogey in round one.
“Definitely a great afternoon on the golf course,” he said. “The wind died a little bit on us so I’m glad to have been able to take advantage of that.
“I hit it really good today. The greens are really firm but I drove it well so I was in fairway most of the time so I could control my ball. I made one or two but, all in all, I just played solid golf today.
“I think the changes on this golf course are good for my game. I, traditionally, have not played that great over here but today I felt like it suited my game a little bit better so I’m looking forward to what this week’s got in store.”
Bekker birdied the fourth and sixth but gave the shot back on the seventh before a gain on the eighth saw him turn in 33.
A birdie on the 11th kick-started his round, as he holed a putt from the fringe on the par-three 12th, made the most of the par-five next and then hit an approach to tap-in range on the 14th to make it four in a row and hit the front.
Earlier, Papadatos made birdies on the first, third and ninth and when he made another gain on the 11th, he led on his own.
A gain on the par-three 16th handed the tournament invite an early two-shot lead but Jacquelin reduced that to one as he came home in 33.
The 44 year old turned in level par with birdies on the second and sixth and bogeys on the fourth and fifth but came to life on the back nine.
He birdied the tenth, 13th and 15th before getting on the par-five last in two for a closing gain.
Home favourites Darren Fichardt and Dylan Frittelli had both reached five under before producing stumbling finishes to fall back into that large group at three under.
An approach to tap-in range had briefly handed Stone a share of the lead at four under after birdies on the tenth, 13th and 14th but he bogeyed the next.
An eagle from 2008 Order of Merit winner Robert Karlsson on the par-five second had also moved him to four under but he bogeyed the next two before almost holing from the fairway on the ninth for a closing birdie.
Scottish pair David Drysdale and Liam Johnston, Norwegian Espen Kofstad, Spaniard Pablo Larrazábal and South Korea's Hyowon Park completed the group three off the lead.