The course was under huge puddles of water on Wednesday and the start of the first round was delayed by three hours, leaving a host of golfers to complete their rounds.
From carded two eagles in his 65, both on par fives, while Bairstow managed eight birdies, his round only spoiled by a dropped shot on the par-four seventh.
Fichardt is also seven under-par with four holes to play, and there are a further five golfers a shot back from the leaders.
"I putted really nicely. I hit a few wedges close and then holed a few putts. It was just a good day," Bairstow said.
"Yesterday, walking down the 16th I thought there was no chance (of playing on Thursday morning) but credit to the green staff for the work they've done and getting it playable."
Around half of the 156-player field need to complete their opening rounds on Friday.
The South African Open is one of golf’s oldest national championships having first been played in 1903.
