He has a two-stroke advantage over South African, 24-year-old Jayden Schaper, who shot eight birdies in a blemish-free round of 64 on Friday to enjoy the early clubhouse lead.
The 25-year-old Chacarra went agonisingly close to opening his round with an albatross from an extraordinary recovery shot.
Instead, he had to settle for an eagle and although he dropped back-to-back shots at the 10th and 11th, he forced his way into the lead with birdies at the 16th and 18th.
Home golfer Branden Grace and Englishman John Parry are in third place on 12 under par, while South Africa's Michael Hollick sits 11 under in joint-fifth place after shooting a bogey-free 63.
That tied the lowest round ever shot at Royal Johannesburg, which Christiaan Burke had achieved along with Chacarra on Thursday.
Burke struggled to a second-round 71 with two bogeys and a double bogey and dropped five shots off the lead.
The lone Australian in the field, Sydney's Austin Bautista, failed to make the cut for the weekend, following up his promising opening three-under 69 with four bogeys in the first six holes on Friday before having to settle for a disappointing two-over 74.
At one under overall, the former Australian No.1-ranked amateur, missed the cut line by two shots.
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