Vettori received the injury in the second match to raise money for tsunami victims here Monday which the World XI won by three wickets and he will miss the deciding Hamilton match on Wednesday.
The left-arm orthodox spinner is one of New Zealand's most potent weapons with 130 One-day International and 178 Test wickets. His injury sees him join fast bowler Shane Bond and all-rounder Jacob Oram on the sidelines due to back problems.
Off-spinner Paul Wiseman has been called in as cover for Vettori after taking 9-13 in a domestic championship match on Monday.
A team spokesman said Vettori felt back pain while bowling during Monday's match.
"We're going to give it 48 hours before it settles down, then a diagnosis can be made," the spokesman said.
Vettori has suffered stress fractures during a series against Australia in 2000 and later the same year in Zimbabwe.
Oram is likely to have a scan later this week for the lower back injury which has ruled him out of cricket since January 9.
Australia are due in New Zealand next month to play five One-dayers and three Tests.