Els carded a second successive seven under par 65 in the morning session to open up a three shot clubhouse lead at Durban Country Club.
The World Number 12 - four times a winner of his national championship - started at the tenth and carded three birdies in an outward 33.
He then pitched his approach to four feet at the third for another birdie, which started a run of four gains in six holes to leave the 41 year old 14 under par.
His nearest challenger in the clubhouse was 19 year old Qualifying School graduate Romain Wattel, the French teenager moving into contention with a six under par 66.
Wattel - who became only the fifth amateur winner on the Challenge Tour last season - chipped in for eagle at the eighth, to go with five birdies and a single bogey.
Goosen joined him on 11 under as the two-time winner of the event gained shots at the eighth, ninth and tenth - and with eight holes remaining there was plenty of time for the double Major winner to put more pressure on his compatriot Els.
Another home favourite - Charl Schwartzel - lies a shot further back on ten under after a round of 69, one ahead of England's David Dixon.
After heavy rain caused most of Thursday's play to be postponed, tournament organisers have decided to cut the field to the top 50 and ties after the second round, with 36 holes to be played on Sunday.
Els said: "It's never easy, but as I said yesterday, I felt really good. Again I feel like I'm hitting the ball quite nicely and that gives you some confidence on the tees.
"I've been doing the same as yesterday and I have a good game-plan for the golf course. Again, the wind didn't blow so it makes low scoring a little easier."
But Els stopped short of predicting what a possible winning score could be, adding: "I don't want to look too far ahead. I'm quite patient this week, I'm playing within myself and I'd like to do that again tomorrow.
"This type of course you can hit one bad shot and make a double quickly. I'll play to my game-plan, keep plugging away and see where it goes."