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
The WRU has teamed up with Crawshay's to tour Georgia in June. The side, which will be called the Crawshays WRU President's XV, will play Emerging Georgia twice, in a tour which supports the Welsh Government's efforts to grow relations between the two countries.
Wales Sevens are looking to re-group after a disappointing tournament last time out in South Africa. The next double leg in New Zealand and Las Vegas offers Gareth Williams a chance to redeem themselves.
Wales Women's head coach Rhys Edwards was at Llandovery to see the conclusion of an entertaining Women's Regional championship where any one of three teams were in contention for title glory on the last day of action.