The Welsh XV had plenty of possession to win the game but did not break the gainline often enough up front or run strongly and directly enough behind.
The Welsh forwards more than held their own but behind the scrum it was the tourists who had the edge in both pace and penetration.
Two of the threequarter line, centre Luke McAlister and wing Joe Rokocoko, played in the under-19 side that won the Junior World Cup in Chile last year and they looked the class players of the night.
Rokocoko made the first try with a powerful blindside surge and well-timed pass to supporting scrum-half Scott Cowan to give New Zealand a 7-6 lead, McAlister kicking the conversion.
Cardiff fly-half Nick MacLeod had kicked two penalties to give Wales a 6-0 lead and his third just before half-time put Wales into a tenuous 9-7 lead at the interval.
McAlister kicked New Zealand back into the lead with a penalty before replacement wing Tony Koonwaiyou dramatically snatched the ball out of the grasp of Llanelli full-back Ceiron Thomas to sprint clear for a try converted by McAlister.
Wales threatened but handled sloppily in the face of aggressive defence. The forwards with hooker Huw Bennett (Swansea) and No 8 James Malpas (Cardiff) continued to make a real game of it.
Wales: Pens - N MacLeod (3). New Zealand: Tries - S Cowan, T Koonwaiyou; cons - L McAlister (2); pen - McAlister.
New Zealand Schools will face Welsh Schools U18 at Neath RFC on Friday 18 January. The match kicks off at 7.15pm
A special video package as Pontypridd claimed the double for the first time in their history by winning the Principality Premiership final, including match build-up, highlights, post match reaction and dressing room celebrations.