"It happened earlier this evening. Jay wanted it to be a really private affair -- close friends and family," the insider told the magazine.
The couple did not issue an official announcement by early Saturday morning.
The media were staked out in front of Jay-Z's Manhattan apartment most of Friday as delivery trucks brought food, candelabras and flowers, and guests including Beyonce's fellow Destiny's Child members Kelly Rowland and Michelle Williams, and the couple's friend Gwyneth Paltrow arrived.
Beyonce's mother Tina Knowles, her father and manager Mathew and her sister Solange also attended the event, People.com said.
The couple had been dating since 2002.