Only a 75th-minute try from All Black wing Joe Rokocoko gave Graham Henry's men a narrow victory as they avoided a repeat of their 1978 defeat at the hands of the same opposition.
Barry Murphy scored Munster's only try, with fly-half Paul Warwick adding 11 points with the boot. All of Munster's points came in an exciting first half and their failure to add to their tally in the second period eventually cost them dear as Rokocoko made the most of his late opportunity.
The 25-year-old, who has 43 tries in 48 internationals for his country, powered through tackles by Peter Stringer and former All Black Doug Howlett after New Zealand had won clean lineout ball deep inside Munster territory.
New Zealand now turn their attentions to Saturday's match with Wales at the Millennium Stadium before their final tour match against England at Twickenham seven days later.
Scorers
Munster 16
Try: Murphy Con: Warwick Pens: Warwick 2 Drop goal: Warwick
New Zealand 18
Tries: Donald, Rokocoko Con: Donald Pens: Donald 2
