The Caribbean boys began their second innings 386 runs behind New Zealand, which declared its first innings at 520/9, and finished in a better position but still 172 runs behind.
After being asked to bat first, Wagner finished with the figures of seven for 39 as the Caribbean side collapsed to be all out for 134 in the first innings, which lasted for mere 45.4 overs.
Speaking on the occasion, ICC Chief Executive David Richardson thanked New Zealand Cricket for hosting the tournament for the third time and extolled the importance of the U-19 Cricket World Cup in grooming players from around the world.
Tim Southee will miss the opening Test against the Windies as he is expecting the birth of his child.
Peru beat New Zealand 2-0 on Wednesday night to win a two-leg playoff and earn the 32nd and last spot in the World Cup field in Russia.
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