Midway through the second half, Leonardo Senatore charged down a Ma'a Nonu kick and gathered the ball to race over for what he believed was a try.
But referee Pascal Gauzere ruled the loose forward had knocked the ball on, although replays showed otherwise.
It was a harsh call on the Pumas who were only 18-6 behind at the time and it left coach Daniel Hourcade wondering what might have been.
"There would have been five points difference and anything could have happened," Hourcade lamented.
Captain Agustin Creevy believed the wrong call had potentially changed the outcome of the game but added diplomatically: "There are things that happen in a game.
Unfortunately the referee didn't see."
New Zealand eventually outscored the Pumas four tries to nil in a match played in difficult wet conditions.
Creevy acknowledged lapses in concentration had also cost his side and that they had not taken their try-scoring chances.
Hourcade highlighted the All Blacks' kicking game as being the difference between the two sides.
Beauden Barrett and Conrad Smith used grubber kicks to set up Julian Savea for the first of his brace, while Barrett, Israel Dagg and Aaron Smith also sent up plenty of contestable kicks which the Pumas struggled to deal with at times.
"If we'd kicked a bit better, as the All Blacks did, [it might have been different]," Hourcade said.
"They do it very well. There is a lot of talk about how well the All Blacks move the ball but I think they are also the best team in the world in terms of kicking. That was the difference between the two teams."