The YouTube video shows a boy dressed in shorts and white shirt running across the stage and approaching the Canadian pop star as he performed on the piano.
A security guard quickly pounced, flung him away from Bieber and knocked the piano partly off stage, as thousands of screaming fans looked on.
The footage shows the boy then being whisked away by two guards and Bieber skipping away to safety on a side of the stage as the music continues to play.
"A young fan desperate to meet his idol did make his way on stage, but was immediately removed and Justin professionally continued with his show," said the concert`s organisers.
"As far as we know, no further action has been taken against the youth."
The 19-year-old singer was performing for the second night in front of thousands of fans at a stadium in Dubai.
Bieber had arrived nearly two hours late for the concert, angering young fans who arrived in Dubai from across the region to see him perform live.(*)