The video for the 45-second long "Pen-Pineapple-Apple-Pen" has been viewed more than 67 million times since hitting YouTube in August, going viral after pop giant Bieber tweeted it as his "favourite video on the internet".
"I'm surprised by this sudden popularity," said the 53-year-old comedian, who goes by Pikotaro, just before receiving the award on Friday at a packed press conference.
"Without Justin's impact, I think only four people would have showed up in this room," he joked.
The video features Pikotaro, dressed in his trademark garish animal print costume, dancing to nonsensical English lyrics such as "I have a pen. I have an apple. Apple pen."
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But despite the global sensation, Pikotaro told reporters that his life had not changed at all since the song became "a worldwide phenomenon" last month.
Pikotaro, who revealed he spent only 100,000 yen ($950) to make the video, hopes to do a world tour though doubts the global craze will continue.