Cole McConchie replaced Santner as a like-for-like replacement, while Kyle Jamieson came in for the rested Lockie Ferguson.
New Zealand faces Canada needing a win to secure a spot in the T20 World Cup Super 8s.
NZ's Santner ruled out after 'dodgy burger' vs Canada
New Zealand's Mitchell Santner has been ruled out of the match against Canada due to illness, described by stand-in captain Daryl Mitchell as a result of a 'dodgy burger.'