New Zealand were 310 for seven at lunch on Friday, with Fleming on 136 not out.
Only 12 overs were possible before lunch, during which New Zealand advanced their total by 45 runs for the loss of one wicket. Fleming added 22 to his overnight score and looked comfortable despite South Africa claiming the second new ball two overs into the day.
Daniel Vettori pulled Ntini's first delivery with the new ball for four but in trying to repeat the shot two balls later he spooned a catch to Andre Nel at mid-on. It was Ntini's fourth wicket of the innings and at lunch he had taken four for 85.
James Franklin joined Fleming and neither left-hander looked in trouble as the South African bowlers failed to find a consistent line and length.
The start of play was again affected by the vagaries of Cape Town's autumn weather. After a delay on the first day because of dew, a portable hovercraft was brought in to dry the outfield, but fog swept over the ground and play only started 55 minutes before lunch, with 83 overs scheduled for the day.
South Africa lead the three-match series 1-0.