No illegal drugs were found on the plane and no charges were brought, but the young singer and his fellow passengers were questioned for several hours, said the source.
The search of the plane was undertaken after U.S. customs officials believed they smelled marijuana on some of Bieber's entourage.
It was not immediately clear who or how many other passengers were on the plane that touched down at New Jersey's Teterboro Airport.
A Port Authority spokesman said his agency was notified at 8:20 p.m. local time (0120 GMT) that Bieber had been released from U.S. Customs, and had no further comment.
Earlier Friday, the Los Angeles County District Attorney's office charged a friend of Bieber's with drug possession in connection with a raid last month on the singer's home in Calabasas, California, about 30 miles (48 km) northeast of Los Angeles.
Xavier Smith, 20, better known as rapper Lil Za, was charged with possession of MDMA and oxycodone and vandalizing the Los Angeles County Sheriff's jail where he was held, said Ricardo Santiago, a spokesman for the district attorney.
Bieber, 19, was arrested last week in Miami Beach on charges of driving under the influence, resisting arrest and driving with an expired license.
The Canadian was also charged on Wednesday with assaulting a limousine driver in Toronto.