The Black Caps right-hander pulled up lame while batting during the second T20 against Pakistan in Hamilton on Sunday night.
He strained his hamstring and will miss the remainder of the series.
The 33-year-old was scheduled to miss the game in Dunedin today anyway, but he will now miss the final two games of the series in Christchurch as well.
Black Caps batting coach Luke Ronchi was able to provide some reassurance for home fans anxious about the upcoming test series against South Africa.
"It is a grade one sort of strain, so it is more like a couple of weeks type of thing," Ronchi said, adding Williamson should be good to go for the two tests against the Proteas.
He also pointed out the Black Caps have got used to doing without their talisman.
"Unfortunately it has been something that is happening a bit, so we’re quite used to that.
"We are quite liking the fact that the guys that have come in are in good touch and are performing domestically."
Central Districts right-hander Will Young has joined the squad as cover, but Ronchi hinted Tim Seifert could slot into the No 3 role.
Whoever gets the nod, they will join a resurgent batting line-up.
The Black Caps have posted scores of 226 for eight and 194 for eight. They lead the series 2-0.
But while the batting has been excellent for the most part, the Black Caps have had a recent tendency to lose too may wickets in the power play, while in Hamilton on Sunday they lost a bucket of wickets at the other end of the innings and missed the opportunity to push well past 200.
"We don’t get too down about certain situations," Ronchi said, adding an innings could be set up in different ways.
"If we play our roles the way we can then hopefully we do see scores like that [today].
"But if the surface is different, and if they bowl differently, then we have to adapt to that and make sure that in each situation the guys are doing what is needed and we’ll see what goes from there."
