The decision confirms spin bowler Ish Sodhi will play his first test in New Zealand after making his debut against Bangladesh in October.
Williamson admitted yesterday his damaged left hand is not 100 per cent two days out from the test at Dunedin's University Oval.
Williamson fractured his left thumb fielding in an ODI in Bangladesh on October 29. The prognosis at the time was he would need six weeks to be ready to play cricket again. That meant the Dunedin test was always going to be touch and go, and so it has proved.
New Zealand side:
Brendon McCullum (c), Corey Anderson, Trent Boult, Peter Fulton, Aaron Redmond, Hamish Rutherford, Ish Sodhi, Tim Southee, Ross Taylor, Neil Wagner, BJ Watling. Doug Bracewell (12th man)