The current world number one had spoken about the incident and said, "For her, it was not a good moment, I was so scared for her, the ball was quick and straight on her".
He broke Carreno Busta on his first service game to immediately take charge, dictating the rallies and forcing his opponent around the court.
Kyrgios had voluntarily asked the Australian Open organisers to schedule all three of his matches this week at the Melbourne Arena.
And to think: Nadal did this after staying up late enough to watch on TV as the man he's chasing in the Grand Slam count, Roger Federer, was pushed to a fifth-set tiebreaker before getting through to the fourth round at almost 1 a.m.
Nadal, a finalist past year when he crashed to Novak Djokovic in straight sets, was far from clinical in his previous match against Federico Delbonis, winning only three out of 20 break points.
After four hours and 26 minutes - the longest match of Kyrgios's career - he collapsed to the court in celebration when Khachanov's final backhand sailed wide.
The Kyrgios serve was on fire early on, sending down four aces in the first two sets. But in the fifth he started to push when he was break down.
Kyrgios held his nerve to prevail 10-8, and will now have to steel himself for an encounter with his Spanish nemesis Nadal.
That feud has been thrust into the spotlight after Kyrgios impersonated Nadal - who has called for the 24-year-old to show more respect - as he was called for a time violation during his second-round win against Gilles Simon at Melbourne Park. "Big difference between today and the previous days", Nadal said.
Australian Open Day 6: Karolina Pliskova latest to fall in third round
The Russian sensed early on that if ever she was going to topple her younger nemesis it would be today. There are upsets and I think it's normal because, yeah, it's tennis and tennis is very unpredictable.
China deploys 450 military medical staff to virus epicentre
Centers for Disease Control (CDC), symptoms of 2019-nCoV may appear in as few as two days or as long as 14 days after exposure. The first human cases were thought to stem from a wholesale market that sold seafood, poultry, farm animals, snakes, and bats.
Google is making ads harder to detect in search results
Many publications have covered their dissatisfaction with the new design and it seems Google has heard this feedback. What do our readers think of the new look? Others say they believe the design was intentional on Google's part.
After his win against Khachanov, an exhausted Kyrgios described the victory as "one of the best of my career." .
'That was insane! I've got no words for how I'm feeling right now'.
"My legs feel about 40 kilos each". Obviously, wasn't easy losing the third, and then losing the fourth, having those match points.
'You think I'm just going to play that slow or what?' Kyrgios argued. "He's (Khachanov) an absolute warrior". Even so, Kyrgios tried to downplay the animosity Saturday, saying: "Whatever happens between us, he's an fantastic player".
As for Nadal, Kyrgios played down any potential fireworks, saying: "He has a winning record against me".
"I'm not thinking about that right now".
'I will do everything I can and hopefully give everything I have and hopefully it will be enough'.
The tennis world will now eagerly await the latest chapter of one of the sport's most antagonistic rivalries when Nadal and Kyrgios face off on Monday.