Nadal got an early break in the match and went on to win the first set 6-3.
However, Kyrgios took excuse with how long the world No 2 was taking between serves.
He felt Nadal was intentionally slowing down the tempo and he let the umpire know on several occasion.
Kyrgios went on the win the second set 6-3 and was quick to his feet to get the match back underway in the third.
But Nadal took his time in his seat and was booed as he walked back onto the court to get play back underway.
At the opposite side of the net, Kyrgios was stood twiddling his racket, indicating he was bored waiting for his rival.
Bad blood has run between Nadal and Kyrgios since their clash at the Mexican Open earlier this year.
After being on the receiving end of several underarm serves, Nadal claimed his opponent “lacks respect.”
And the Spaniard refused to call a truce when asked about those comments earlier this week.
“My thoughts are very clear, no?” he said.
“I play against a top talent player, very dangerous player when he wants to play tennis.
“Normally against the best players, he wants to play tennis. When that happens, he’s a very dangerous opponent.
“Of course, like second round is a super tough one. I know that. I need to be at my 100 per cent. I’m going to fight for it.”