And the three-time Major winner will be aiming for another similar effort later this afternoon as he bids to secure a fifth title.
The South African carded a five under par round of 64 after just 17 holes were being used at the Durban Country Club due to the par three fourth hole being rendered unplayable - to move on to 19 under overall.
He now faces what is looking like a straight fight with fellow countryman and two-time former winner Retief Goosen, who is a stroke back after a six under 63 score.
The tournament, already heavily affected by rain after persistent showers forced most of day one to be abandoned, experienced more trouble when a sharp downpour made the fourth green unplayable.
It means that instead of playing 36 holes today, only 34 will be played in what is now a 70 hole competition at the normally par 72 course.
And Els and Goosen will be difficult to catch as both looked in fine form in the co-sanctioned European and Sunshine Tour event as they aimed to end recent title droughts.
Goosen, a two-time US Open Championship winner, said: "We're both playing solid, there were a couple of bad holes out there and also some good holes. Hopefully we can keep it going."
Current Open Champion Louis Oosthuizen is the closest to them after a five under 64 took him to 15 under, while another rising South African star, Charl Schwartzel, is on 13 under following his 66.
Three players are a further shot back - Martin Maritz (65) as well as French duo Victor Riu (65) and Romain Wattel (68) - while Robert Rock is the highest placed Englishman.
He recorded a five under par round of 64 and is in a group of four players on 11 under with Alexander Cejka (66), Tim Clark (65) and Thorbjorn Olesen (65) beside him.
Reflecting on his chances in the tournament, Rock said: "I don't think there's much of a chance of winning, but there's a decent chance of making a top ten or top five finish, unless I shoot a really, really low round this afternoon.
"I was a bit rushed this morning, so it was nice to shoot a decent score."