The home favourites had been locked together at 12 under par when play was suspended for one hour and 50 minutes due to a dangerous weather situation on Friday afternoon, with talented 20-year-old Nienaber on the 15th green and Blaauw two holes further down the course.
But Blaauw was able to hole his 20 foot birdie putt on the 17th green when play resumed, before safely parring the last to sign for a sensational 63 and head into the weekend on 13 under.
First round co-leader Nienaber, meanwhile, bogeyed the 16th to slip two shots behind Blaauw but got the shot back on the par three 17th and parred the 18th to finish the day in second place on 12 under.
Just under 40 afternoon starters had holes still to complete when the players were called off the course at Randpark Golf Club due to fading light on Friday evening, and they will return to finish their second rounds at 7.00am on Saturday.
Shaun Norris, who had led alongside Nienaber on Thursday, was on nine under with three holes still to play.
Blaauw, who began the day three shots off the lead, opened his second round with a birdie but gave the shot straight back at the difficult second hole.
After making a gain at the long fourth, Blaauw got another from eight feet on the sixth to move to seven under.
The 34-year-old then closed the front nine with a ten foot birdie on the ninth before reeling off back to back gains on the 11th and 12th.
And when he holed a lengthy eagle putt on the par five 14th, Blaauw moved to 12 under.
He gave himself another birdie chance at the 16th but his 12 foot effort hit the hole and did not drop.
Blaauw had sent his tee shot at the par three 17th to within 20 feet of the pin just before the hooter sounded at 3.50pm local time.
And when play resumed at 5.40pm, he converted the putt to take the outright lead.
Blaauw was pleased to be able to finish his round on Friday. He said: “I’m just happy that I don’t have to come out tomorrow morning but the cherry on top is the 63 so I’m very happy.
“I hit it very well. From fairway to green I hit it very, very well and then obviously made some putts – that is very key.
“I made just one bogey today and obviously you want to keep the bogeys off your card. And I hit a nice, nice bonus eagle on the 14th, which I’m very chuffed about.
“I can’t think ahead. Yes, you always want to think you’re going to raise the cup. But to be honest there are two more rounds to go. Golf is obviously the job so I need to get that job done.”
Nienaber did not get off to the best of starts, dropping a shot at the second after failing to get on the green in two.
But he bounced back in style, notching birdies at each of the next three holes to grab a share of the lead.
After a good par save from around eight feet at the eighth, the big hitting youngster holed his 18 foot birdie putt on the ninth to move to 11 under.
Nienaber got into tree trouble off the tenth tee but went on to make a valuable par thanks to a lovely third shot.
He gave himself an unlikely birdie opportunity at the long 12th after playing a delightful third shot from the other side of the third tee, but he was not able to hole his putt from the fringe.
Nienaber took advantage of the long 14th from close range to grab a share of the lead alongside countryman Blaauw before the suspension.
But he went on to make his second bogey of the day on the 16th after the restart.
Nienaber made amends at the 17th, though, firing a birdie on his way to a second round 67.
He said: “(A delay) is never nice but I think I had it on the part of the course where I really didn’t want it.
“The 18th, 17th, 16th and 15th are quite tough, without having to start on them.
“But I got through it and I finished so I’m happy.
“I’ve really put myself in a good position so I’m really excited to see what happens tomorrow and the day after.”