It happened while Phehlukwayo was batting during the second one-day international in Durban on Tuesday.
Sarfraz, Pakistan's wicketkeeper, was heard on a stump microphone saying in the Urdu language: "Hey black man, where is your mother sitting today? What (prayer) have you got her to say for you today?"
The comment was apparently in reference to a couple of lucky escapes for Phehlukwayo as he made a career-best score of 69 not out to help South Africa win. Phehlukwayo had just got an inside edge and the ball narrowly missed his stumps when Sarfraz made the comments. Sarfraz was not close to Phehlukwayo and there was no confrontation.
Sarfraz apologized on Twitter on Wednesday, writing that his outburst was an "expression of frustration" and "not directed towards anyone in particular" despite Phehlukwayo being the only black player on the field at the time.
"I certainly had no intention of upsetting anyone," Sarfraz wrote. "I did not even mean for my words to be heard, understood or communicated to the opposing team or the cricket fans."
But the Pakistan Cricket Board rebuked Sarfraz in a statement and said it had a "zero-tolerance approach towards racist comments made; in whatever context."
"Sarfraz is one of the most respected cricketers in the world," the PCB said. "However, captaining Pakistan is a massive honor and any hurtful remarks by any cricketer, let alone the captain, are not acceptable to the PCB."
The PCB did not announce any sanction for Sarfraz.
The games between the teams have generally been played in a good spirit. South Africa won the test series 3-0. The five-match one-day series is level at 1-1 ahead of the third game on Friday.