"Why would I apologize? I won the point," said Kyrgios after his four-set second-round defeat, BBC Sport reported.
"I was going for him. I wanted to hit him.
"The dude has got how many Slams, how much money in the bank account? I think he can take a ball to the chest."
Nadal managed to get his racquet in the way but said the shot was "dangerous".
"It is not dangerous for me, it is dangerous for a line referee, dangerous for a crowd," the Spaniard said.
"When you hit the ball like this, you don't know where the ball goes.
"I know he's a big talented player, but I am a professional player too. I know when you hit this kind of ball, the ball can go anywhere."
It was only one flashpoint in a stormy 6-3, 3-6, 7-6 (7-5), 7-6 (7-3) win for two-time champion Nadal.
The pair met on Centre Court five years ago when a 19-year-old Kyrgios, ranked 144th in the world, pulled off a shock four-set victory over the then world number one.
Before Thursday's encounter their head-to-head record stood at three wins apiece, with Kyrgios winning a testy encounter in Acapulco in February.
In the wake of that win, the Australian had described Nadal as "super salty" in defeat and admitted earlier in the Championships that the pair would not be sharing a drink any time soon.
Underarm, but underhand?
One of the flashpoints in his win in Mexico had been Kyrgios' decision to serve underarm. He produced the same tactic twice on Centre Court, winning the point on each occasion.
He was asked afterward why he did not attempt it more often with Nadal standing deep behind the baseline to field a serve that delivered 29 aces.
"If I do something outrageous, I get destroyed in the media for it. I thought I'd be professional and hit a normal serve. That's what I was thinking," he said
"No, I'm kidding. I just didn't want to hit another one. Oh, shoot me down for not hitting an underarm serve Centre Court against Rafa.
"What do you want from me, man? I don't know what you want from me."
Clashes with officialdom
During the first half of the match, Kyrgios repeatedly argued with umpire Damien Dumusois, mainly about the time that Nadal was taking between points.
Kyrgios described the official as "a disgrace" during the match and his opinion had not mellowed in the aftermath.
"The umpire today was horrendous. I mean, he was terrible,
"The rule is like play to the speed of the server. Why do I have to wait for Rafa to get into his rhythm every time?
"I thought the way he handled the match was just bad."