The order from match referee Clive Lloyd came after the South Africans said they had taken photographs of the pitch following an overheard conversation which suggested the groundsman was about to carry out illegal repairs.
South Africa coach Eric Simons said he and other members of the touring party had inspected the pitch after the second day on Thursday.
"We saw that the pitch had been broken up and was pretty serious," Simons said. "As we turned to leave we overheard a conversation which made us nervous, so we took some photographs.
"We came in this morning and had another look and noticed some work had been done, which was obviously not correct and the match referee corrected that before play."
The laws of cricket rule that no remedial work on a pitch can be carried out during a match.
Match referee Lloyd said there had been a "miscommunication" between the umpires and groundsman Karl Johnson, who believed he had been instructed "to secure several loose pieces of turf back in place" outside the right-hander's leg stump.
"Before the start of play today (Friday) I instructed that the pitch be returned to the condition it was in at the close of play."
South Africa pace bowler Andre Nel was officially warned on Thursday for running on the pitch after bowling two balls.
Simons added: "We were very surprised the work had been done. Nothing like this has happened to us before."
He would not reveal details of the overhead conversation but added: "It was a bit distracting, but it didn't really affect the state of the game. From our perspective the matter is over."
New Zealand ended the third day on 361 for seven, 98 runs behind South Africa's 459.
