"One time, maybe you could have got away with this, but you can't do that now," Judge Anthony Walsh told the 33-year-old man on Wednesday.
"You must understand that what you did amounted to an assault. Our law has been amended so that children are protected," the Wairarapa Times-Age newspaper reported him saying.
A new law was passed in May, removing a provision allowing parents to use "reasonable force" in disciplining their children.
Opponents of the law said the conviction of the man, who was sentenced to nine months supervision including undergoing anger management, showed the law was "parents' worst nightmare."
The court was told the boy received a bruised shoulder when his father roughly grabbed him before smacking his bottom three times with his open hand after he had misbehaved at school.
The boy's mother took a photograph of the bruise and showed it to a relative, who later reported it to police.
Bob McCoskrie, director of the conservative lobby group Family First New Zealand said the new law had created a "paranoid parenting environment".
"This case has confirmed Kiwi parents' worst nightmare."
Child advocacy group Barnardo's New Zealand welcomed the court's decision.
"I believe this is the first reported case in which the new law relating to child discipline in the home has been tested in court and the law has worked well," acting chief executive Peter Gerrie said.
It showed that parents had to accept non-violent ways of disciplining their children, he said.