But the Heineken Cup champions, short 10 of their first choice players due to Ireland's autumn Tests, leaked a crucial 76th minute try from Joe Rokocoko that got the tourists out of jail.
Munster coach Tony McGahan and captain for the night Mick O'Driscoll will take whatever positives they can from the game, but O'Driscoll, in particular, was hard to console.
"We possibly deserved more from the game. To lose by two points to probably the best side in the world with 10 or 11 of our players missing, you would probably take it," O'Driscoll said.
"We were playing New Zealand so you don't need anyone to tell you who you are playing. It is a privilege to play New Zealand.
"You don't need any more inspiration to play these boys. We came so close but yet so far. Certainly for fat lugs like me you don't know what is going on all the time.
"All you remember at the end of the day is the result and we were beaten."
O'Driscoll, who led his side superbly and put in a tireless individual display, can take much from his own display and that of other 19 Munster players who graced the pitch.
Half-backs Paul Warwick and Peter Stringer hardly put a foot wrong all night, young prop Timmy Ryan looked right at home on his first start for Munster and back rowers Niall Ronan, James Coughlan and Billy Holland were immense throughout.
There were heroes dotted all over the pitch for Munster and O'Driscoll acknowledged their efforts afterwards.
"It is very special to play an international team. We were massive underdogs going in and I think the heart and commitment that the boys showed on the pitch and the coaching staff for the last few weeks makes you very proud to be a Munster man (tonight).
"Fair play to New Zealand, they were a better side on the night and you gotta live with that."
Australian McGahan hailed the efforts of his players, whose collective performance was all the more impressive considering they had not played since losing to Ulster in the Magners League on October 24.
"The guys should keep the result and be immensely proud of the way they played," he said.
"We were still in it until the 60th or 70th minute but you could see how tired the lads were. We were holding onto that (16-13) lead but just couldn't hold on long enough."
Asked about some of the refereeing decisions that did not go Munster's way, particularly the ones in the latter stages of the second half, McGahan was philosophical about their influence.
"The game goes in ebbs and flows, but the back end of that game you could see how tired the boys were, tearing across the back-line there, the cramps they were getting.
"You were looking for the close decisions to go your way but it wasn't happening.
"The crowd were behind us, there's a massive upset in the balance, I think you can be influenced by all that, but if you watch it afterwards, I think all those things even themselves out.
"It would have been nice to get them, we didn't and the scoreline sits."
Meanwhile, New Zealand coach Graham Henry paid tribute to the Munster players, when visiting their dressing room, telling them 'you've written another chapter in this legendary Munster story. I know you didn't win but you can be hugely proud of what you've achieved tonight.'
From an All Blacks perspective, Henry said his young players will be all the better for having to dig deep and find a late try to win in the cauldron of Thomond Park.
"Our team are young guys and it was a good experience for them, very good for their rugby development. To be under that kind of pressure (and win) is immense for them," he said.
"They will have learned a lot playing in that kind of atmosphere. I haven't been in an atmosphere like that very often."
Munster included four New Zealanders in their squad and Doug Howlett, Rua Tipoki, Lifeimi Mafi and Jeremy Manning threw down the gauntlet pre-match by performing their own four-man haka before the All Blacks could respond.
"It shows the spirit of the Munster team and the geographic area it represents. It was a nice to have a win but I think the occasion was more important," Henry admitted.
"I think we played a lot of the rugby. We tried to be constructive most of the time. It was a very young inexperienced All Black side.
"It was one of those games where we just had to hang in and hope we could score a winning try. But we had opportunities."