"He needs further rehab on his wrist," coach Mike Hesson said yesterday. "This is not the time of year we want to rush him. He has batted the last couple of days without huge discomfort."
Williamson suffered a small tear to a ligament. He has had injections and is close to being right. Hesson is sure Williamson will be fit for the start of the test series against Pakistan in Abu Dhabi on November 11.
Ordinarily injuries can be handled satisfactorily, providing they arrive in single file.
However, with senior batsman Ross Taylor - who comes in at No4, one spot behind Williamson - already rubbed out of the series with a calf injury, it leaves New Zealand vulnerable in one area of the game.
"We're just not risking him, or Ross. It's a huge season for us and this is the first part so we won't compromise the rest of it," Hesson said.
Then again, a different slant is that it offers opportunities to others.
In this case, Dean Brownlie and Tom Latham, at Nos3 and 5 respectively in the opening six-wicket loss to South Africa on Tuesday, are expected to get another chance, either side of captain Brendon McCullum in the order.
Latham is an opening option too. It is his test batting position and he's sure to get a chance in the count down to the naming of the New Zealand World Cup squad in early January.
However, Jimmy Neesham is expected to have another turn at the top tomorrow, after showing encouraging signs in a run-a-ball, but all too brief, 16 on Tuesday.
With a question mark over Williamson's bowling action still to be cleared, New Zealand need a sixth bowler batting somewhere in the top six, which works in Neesham's favour for now.
"That's probably my position [No5] for this series," Latham said yesterday.
"I've been asked to do a job in the middle order and hopefully I can do that in the next two games."
Rushing to judgments this early in World Cup summer would be rash. But team management will want to see rapid progress from their batsmen tomorrow.
Opener Martin Guptill's five off 29 balls on Tuesday wasn't a lusty start, but Hesson believes that his touch, and clean striking ability will return with confidence.
"He's probably searching for a bit of form. He's more than capable of playing match-winning innings for us," Hesson said.
The bowlers were generally tidy on Tuesday, and with Southee to return tomorrow - and the fielding in sharp form - those elements of the game are in solid shape.
South Africa took a day off yesterday, several players heading to the golf course.
Before teeing off, lefthander JP Duminy, whose unbeaten 58, in concert with captain AB de Villiers' 89 not out, completed the win on Tuesday, acknowledged New Zealand's work with the ball and in the field.
"They're a very street-smart side the way they go about their bowling side of things," Duminy said. "And their fielding is one of the best in the world."
So, two out of three ain't bad.
3 Problems for NZ to ponder
1 Dale Steyn
The world's best fast bowler, with a terrific record and a fierce will to succeed. Doesn't particularly like being hit by batsmen.
2 Vernon Philander
Dead-eye seamer back after missing South Africa's recent tri-series. Opener Martin Guptill got two runs off 16 Philander deliveries on Tuesday.
3 Morne Morkel
The tall guy who guarantees bounce. Awkward customer and ideal counterpoint to the methods of Steyn and Philander.