Australian Dimitrios Papadatos began his last chance of 2018 to secure a European Tour card with an impressive 67 at the Alfred Dunhill Championship in South Africa.
The South African native put together four straight birdies on the back nine to overtake Papadatos, who sat atop the leaderboard for much of the afternoon.
French veteran Raphael Jacquelin recovered from an uncertain start as he bogeyed the fourth and fifth before a birdie at the sixth and four more gains on the back nine lifted him to four under, while defending champion Brandon Stone is among a group of eight players who are three off the lead.
Bekker took pole position through the opening 18 holes after battling initial strong winds to reach a six-under 66 at the Leopard Creek Country Club on Thursday.
Favourite Charl Schwartzel of South Africa, a four-time victor of the Dunhill Championship, could manage only one birdie as he began with a one-over 73.
Bekker was fortunate to play when the wind died down.
"I hit it really good". The greens were quite firm and fast so yes, I was very happy with that round.
"It was definitely a great afternoon on the golf course", said Bekker, an eight-time victor on the Sunshine Tour.
"I think the changes on this golf course are good for my game". I, traditionally, have not played that great over here but I felt like it suited my game a little bit better.
Among those on 69 is defending champion Brandon Stone while Louis Oosthuizen, victor of his first South African Open title last Sunday, carded a 71.