Da Silva ended on 10 under par after holing stunning chip shots on the 15th and 18th holes to assume a commanding lead over second-placed Jaco van Zyl.
The Brazilian admitted that his late start on Thursday – after a nearly three-hour delay for high winds brought an end to play – gave him an advantage over the morning field.
“I got a good break yesterday,” he said. “It was extremely hard out there for the morning field, and then I got the break and I just started making some putts.”
“I somehow just felt the pace, and my caddie and I are reading the greens very well,” he added. “My putting has been letting me down lately, and it just came alive.”
Da Silva’s round was his best ever as a professional, surpassing his effort of 63 in the closing round of the Sun City Golf Challenge in 2011.
The second round of the Africa Open got under way on Friday as players battled to make up the time lost on Thursday.