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
Sam Cross and Luke Treharne have been named as co-captains of the Wales Sevens side as head coach Gareth Williams names his 12-man squad to play in the first leg of the HSBC World Series in Dubai next weekend.
Bedwas head coach Steve Law and players Nicky Griffiths and Alun Rees extol the virtues of the close knit club as they prepare to host third place RGC 1404 - who are one place head of them on the Principality Premiership points table - on Saturday.
Many of the Wales squad have said Diolch (thank you) to someone who played an important part in their early playing days by nominating them to be invited to the Wales v South Africa match. One person, Gowerton Comprehensive geography teacher Mr Dean Mason was nominated by two of his former pupils, Dan Biggar and Sam Davies.
The second WRU disability rugby pilot has been delivered, this time in Caerphilly schools, culminating in a festival at the Caerphilly Centre of Sporting Excellence, Ystrad Mynach tomorrow. Plans are in place to set up a Disability Rugby Club in Newbridge to provide long-term playing opportunities.
WRU TV: Hear from inside the Wales camp as Neil Jenkins discusses this weekend's clash with South Africa and how the squad are looking to put in a strong performance to round of the 2016 Under Armour Series