The Canadian pop sensation was at the piano during the final few minutes of his concert, when a youth ran onto the stage, past the security, and grabbed him from behind.
Bieber was able to extract himself, while security personnel dashed on to nab the attacker, who managed to knock over the piano.
Bieber carried on performing amid the mayhem, while security guards righted the piano.
The singer later tweeted: "Dubai. Nothing stops the show. 2 more to go." He next plays in Cape Town, South Africa.
The 19-year-old took a three-minute break after the on-stage fracas before returning to sing Boyfriend and then Baby.
His guitarist and musical director Dan Kanter later tweeted: "It wasn't a prank. Someone ran on stage during Believe and the piano got knocked off its platform. Everyone is fine. No need to worry!"
- Justin Bieber's antics, a sign of the crushing power of fame?
It was a rough 24 hours for Bieber, who turned up two hours and 20 minutes late for his second show in Dubai, the second night in a row he had a late start. The long wait during the Saturday concert had frustrated fans taking to Twitter to vent their anger.
In an unrelated development, two Virginia songwriters filed a lawsuit Thursday against Justin Bieber and Usher for copyright infringement on the 2010 song Somebody to Love.
Devin Copeland and Mareio Overton claim Bieber's song contains numerous lyrical and stylistic similarities to the song they wrote in 2008 by the same name.
Bieber has drawn attention for erratic behaviour as he tours Europe with the Believe tour.
He walked through an airport with his shirt off in Poland, evaded airport security in Turkey and upset Anne Frank fans with an inappropriate comment in the guest book of Anne Frank House in Amsterdam.
The Canadian singer wrote: "Truly inspiring to be able to come here. Anne was a great girl. Hopefully she would have been a belieber."
The museum defended the star for his interest in the museum but added his comment "wasn't very sensible."