Smith said that while Mitchell Marsh was legitimately caught and bowled he should not have been given out because the umpires were reacting to crowd pressure.
There were heated exchanges on the field between the New Zealanders and Australians after Marsh was bizarrely dismissed when the ball ricocheted from his bat to his foot then back to the bowler Matt Henry.
It ignited a batting collapse that saw Australia lose their last five wickets for 27 runs to lose the match and allow New Zealand to take the series 2-1.
The umpires only took action when the crowd reacted vociferously to a replay on the big screen which showed the ball had not hit the ground.
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The Australian media dubbed it a dismissal by "mob rule" and Smith said he believed the system was wrong.
"My thoughts are still the same as last night, the whole process of it needs to improve," the Australian captain said when reviewing the match on Tuesday.
"I don't think there should be a replay on the screen before the next ball's bowled. I don't think that's how a decision should be made."
"We both play a good, hard, aggressive brand of cricket. It's going to be another tough series," he said.
"I think we are all happy with the way the game is being played. It's been played hard and fair throughout this series, like it always is with Australia and New Zealand and I'm sure it's going to continue to be the same in the Test series."
New Zealand captain Brendon McCullum, who was playing his final ODI after a distinguished 260-match career, said the umpires' concern was whether New Zealand had actually appealed for Marsh to be given out.
McCullum added it was disappointing that the controversy had detracted from the New Zealand victory.
But he added: "To walk away beating the world champions in the Chappell-Hadlee series which means so much to us is a fitting way to step away from the game.