While the Sunshine Tour professionals battled the elements at Arabella Golf Estate on the Vodacom Origins of Golf presented by Samsung, Bekker enjoyed the mild weather in Russia and shot 67 along with six others to join a traffic jam at the top of the leaderboard.
Tournament hopefuls Gagnjeet Bhullar and Maximilian Kieffer tied for the lead along with South African Louis de Jager, who birdied the 17th and 18th on his way to a share of the lead.
But Bekker was the man who set the pace after he started on the 10th and turned at four-under without so much as a drop on his card. The three-time Sunshine Tour champion went into cruise control after turning in 32 and, despite making a lone drop at the fifth, shot five-under for the round to set the clubhouse lead.
De Jager turned with a steady two-under-par front nine, but he began to attack on the back stretch and was rewarded with gains at the 11th and 13th. A bogey at the 14th could have derailed the charge, but the 27-year-old has been touring since 2008 and regrouped like a seasoned veteran.
After making regulation pars at the 15th and 16th he birdied the 17th and added a cherry on top at the 18th for his share of the lead.
Pre-tournament favourite Scott Jamieson, who won the inaugural Nelson Mandela Championship in 2012, had turned in three-under-par at the halfway mark of his round. The number to beat was 67 and two South Africans had put it up there for the Scot to chase.