Guptill was one of the best Black Caps performers in the opening match of the Chappell-Hadlee Trophy on Monday (Jan 30) in Auckland, scoring 61 as New Zealand posted a six-run win.
Coach Mike Hesson said Guptill had suffered a minor hamstring strain while fielding and would sit out the next match in Napier as a precaution.
"After being monitored over the last 24 hours it's become apparent he won't quite be ready for Napier," Hesson said.
"He'll remain with the team and we'll continue to monitor him ahead of the third ODI in Hamilton."
Northern Districts batsman Dean Brownlie, who last played for New Zealand in December 2014, has been called in as a replacement.