Substitute Ben Waine scored the winner in his first senior international game for New Zealand from a free kick in the 75th minute.
The Wellington Phoenix player had only been on the field for less than 10 minutes when he scored from close range.
Papua New Guinea had not played an international fixture since 2019, whereas the All Whites last played in January.
The Kapuls are ranked 165 on Fifa's ranking, more than 50 places below New Zealand (111).
New Zealand had several chances to score late in the game but could not convert.