The music producer and rapper was born and raised in Brooklyn and joined the Canadian heartthrob during his performance in his hometown as part of his Believe tour on Monday night
Justin tweeted: "meant alot to have the man himself come show love tonight. thanks @JayZ ...happy to be in Brooklyn today."
Fans took to the social networking site to express their delight at the live collaboration.
Lauren from California wrote: "so crazy our small town boy from Canada had the JAYZ at his show @Justinbieber #proud of you #bieberinbrooklyn."
Another fan from New York tweeted: "#BIEBERinBROOKLYN WAS THE BEST EVER. JUSTIN WAS SO HAPPY THROUGHOUT THE WHOLE THING".
During the show Justin sang a cover of Justin Timberlake's hit Cry Me A River, which he released after his split from Britney Spears. Bieber is yet to confirm if he has split from girlfriend Selena Gomez, but their romance is thought to be over.
The 18-year-old singer is now busy rehearsing for his performance at the AMA Awards in Los Angeles later this week.