The England team management released a statement to confirm Stokes' injury.
The 33-year-old, who had sustained a torn hamstring on the same left leg in August this year, was forced to walk off the field midway through the day due to apparent discomfort.
Stokes seemed to be in pain after delivering the second ball of his third over and immediately headed towards the dressing room.
The England team management released a statement confirming that Stokes was receiving treatment for a left hamstring issue and would not return to the field during New Zealand's innings. His availability for England's second innings will be determined after further assessment.
This setback comes after the hamstring tear ruled him out of the entire three-Test series against Sri Lanka at home in August-September. He was only deemed fit enough to join the tour of Pakistan from the second Test onwards in October
Despite the Hamilton Test being a dead rubber, with England having already secured the series 2-0, Stokes has taken on a significant seam bowling workload.
His 24 overs in New Zealand's first innings were the most he has bowled in a single day throughout his 110-Test career. Moreover, his 66.3 overs across three Tests are the most he has sent down in a series as captain.
While the extent of Stokes's latest injury remains uncertain, the team management will closely monitor him and make a decision regarding his participation in the remainder of the match.