Bothma, who closed a first-round, 8-under 64 Friday morning, came back with a 1-under 71 Friday afternoon to move to 9-under-par 135. That was good enough for the clubhouse lead at Leopard Creek Country Club.
The tournament had a weather delay of over two hours on Thursday and is still trying to catch up. The second round will be completed on Saturday with the third round to begin shortly thereafter. However, there are more storms in the forecast for Saturday.
Titch Moore carded his second straight round of 4-under 68 to move into a tie for second place at 8-under-par 136. He was joined there by Phillip Archer (70) and Louis Oosthuizen (67)
Charl Schwartzel, the defending champion, posted a 5-under 67. He shares fifth place with Sean Farrell, James Kingston, Doug McGuigan, Nic Henning and Grant Veenstra at minus-7.
Ernie Els also posted a 67 to climb into contention at 6-under-par 138. He ran off three straight birdies from the 13th, his fourth, to get his round going. The South African birdied the 18th and second to get to minus-6.
Bothma played the final seven holes of his first round Friday morning and picked up three birdies in those seven holes to lead after round one at 8 under.
The South African returned to the front nine to begin his second round and picked up right where he left off. Bothma birdied the par-5 second for the second straight round.
He then birdied five and six, each for the second time, to move to 11 under. Bothma dropped a shot on the seventh, but came back to birdie the par-4 ninth.
Bothma struggled on the back nine. He tripped to another bogey on the par-3 12th. The 32-year-old faltered to a double bogey at the par-5 15th to drop to 8 under. He got that stroke back with a birdie on 17 before a par at the last.
'I've got the flu so I just wanted to get through my round,' Bothma said. 'I was quite nonchalant. I didn't go for the big shots - just went for the middle of the green and now and then I pulled or pushed one close to the hole.'
Oosthuizen got off to a flying start with three birdies in his first four holes. He bogeyed the seventh, but atoned for that mistake with a birdie on the ninth. Around the turn, he posted three more birdies and a bogey to jump from 12th to a share of second.
Moore started his second round on the 10th tee at Leopard Creek. After a birdie on the par-4 10th, he bogeyed 12 and 13. Moore got those shots back thanks to three birdies in a four-hole stretch from the 15th. He played the front nine in minus-2 with seven pars and two birdies.
Archer was alone in second after round one. He played the back nine in 1 over as he bogeyed the 18th, his ninth. Archer birdied the second and fourth to get to seven-under. He picked up a birdie on No. 8 to share second place.
Els is tied for 11th place at minus-6. He stands alongside Alan Michell (68), Trevor Immelman (69) and Stephen Scahill (66).
The closest players to the leaders still on the course are Justin Walters and Thomas Aiken. Each are minus-4 through 15 holes.