"Yeah, I just told him what I thought," said Kyrgios when questioned about the incident at his post-match press conference.
"I don't think he controlled the match well. "He let a guy throw a ball back into play, which for me is pretty unprofessional.
"And as I said previously, with music playing during points, that's the first time I've ever seen it happen."
Kyrgios's demise leaves Bernard Tomic and John Millman as the only Australian men in the singles draw.
They meet in a third-round clash on Saturday evening.
Kyrgios, a quarter-finalist last year, looked to be perilously close to unravelling in the ninth game of the second set when he repeatedly complained to Keothavong that he was being distracted by music coming from somewhere in the crowd at Rod Laver Arena.
"Do you want to stop? We can stop," responded Keothavong, although it was unclear whether the Australian heard him.
"Mate, there is music playing in the crowd and while we are playing - I've told you seven times," Kyrgios complained a couple of points later.
"Just answer the question. "Is music allowed to be played while we are playing? Am I hearing things? "It's a circus."
Shortly afterwards, Kyrgios found himself down two sets to love and seemingly in all sorts of trouble.
But the third set was a complete turnaround, with Kyrgios racing to a 5-0 lead before claiming it 6-1.
Games stayed on serve until the 10th game of the final set, when Berdych broke to claim the victory.
"That's why he's a top player, he steadies the ship, he gets back to it and takes his time, starts serving at a high level again and starts making clutch shots at crucial times," Kyrgios said.
"I thought if I grabbed the fourth (set) I would win the fifth. "I felt fine physically, but I didn't take it there."
Berdych next plays Spain's No.24 seed Roberto Bautista Agut, who upset No.12 seed and 2014 US Open champion Marin Cilic from Croatia 6-4 7-6 (7-5) 7-5.
The Czech was a semi-finalist at Melbourne Park in 2014 and 2015, and a quarter-finalist in each of the three years prior to that.
"It was a difficult match," Berdych said. "I have already played quite a few of those and I have a lot of experience playing Davis Cup matches or tough matches like that. "I tried to remain composed and not look too much over the net."
-AAP