The batsman picked up a calf strain while preparing for the first-class game with Auckland and could be out for up to six weeks. Guptill ruled out due to calf injury against Pakistan in the UAE.
The Black Caps will face Pakistan in three T20Is and three ODIs starting from 31 October.
New Zealand selector Gavin Larsen said: “Unfortunately for Martin, it will take him some time to get over this injury.
“And, with a long summer ahead, we need to make sure we minimize the risk of him repeating it.”
New Zealand will also play three Tests after the limited-overs leg of the tour and will be without first-choice spinner Mitchell Santner, who is still recovering from a long-term knee injury.