Bieber, 17, said on his Twitter page: "Got my friend @seankingston in my prayers tonight. a true friend and big bro. please keep him in your prayers tonight as well."
The two singers have become close friends and recently collaborated on the single "Eenie Meenie".
Kingston, 21, was rushed to Miami Beach Hospital following a serious jet ski accident in which he collided with a bridge at high speed.
Initially in serious condition, it has been reported that Kingston's condition has since stabilised and he has responded well to treatment.
A boat passing by found Kingston floating in the water just moments after the crash and pulled him out of the water.
Kingston's representative released a statement soon after he was taken to hospital: "Sean Kingston was in an accident today. No further details are available at the moment. He and his family thank everyone for the well-wishes."
Kingston is a popular singer, most famous for his hit song "Beautiful Girls". Other celebrity friends have followed Bieber in sending their best wishes and prayers to Kingston and his family. Rihanna tweeted: "Sean we praying for u baby."
Nicki Minaj said on Twitter: "My love & prayers are with Sean Kingston & his family."
LL Cool J also tweeted: "I hope and pray that Sean Kingston recovers quickly….#staystrong."
Giving an update on Kingston's condition, friend James Rosemond (aka "LilHenchmen") said: "Just left the hospital and great news my big bro @seankingston is doing fine..Thanks to all the prayers and the love. WE LOVE YOU BRO!"