The 16-year-old's single 'Baby', featuring Ludacris, has clocked up more than 250 million hits, usurping Gaga into second place with 247.6 million views.
The singer thanked his fans on Twitter before praising his rival, adding: "I just need to say that @ladygaga is an incredible artist who have great respect for. And her vid is incredible.
"Thank you all for caring. Just want you to know I care too and I'm just a normal kid. Thanks."
Bieber recently witnessed the downside of his online popularity, when a vote on his site was hijacked suggesting the singer should tour North Korea, though he has since said he will not honour the online poll.
