Michael carded four birdies and one bogey in a second round of 69 at Pretoria Country Club to finish 7-under-par, with scoring again proving difficult on a course measuring just 6,830 yards.
Overnight leader Harding started his second round on the back nine and bogeyed 10 and 11, but bounced back in spectacular fashion by holing his tee shot with a wedge on the 141-yard 14th.
That took Harding back into a share of the lead before a bogey on the difficult 18th dropped him back to 6-under, two ahead of American Daniel Im, who had earlier completed a second successive 68.
Pre-tournament favourite Charl Schwartzel was a shot further back after birdies on the first and ninth, the former Masters champion slowly playing his way back into form after the longest break of his career over the winter.
Schwartzel holed from 20 feet for an eagle on the par-five 12th and just two feet for birdie on the next and at 4-under par, was suddenly into a share of second place.
That was because Harding had found trouble off the tee on the fourth to run up a double bogey six, before a bogey on the next dropped him back to 3-under.
Schwartzel chipped in for a birdie on the 15th to move into outright second on 5-under par, but still had one hole remaining when play was suspended at 4:48pm local time due to the threat of lightning.