"He's just a really big flirt," one friend told the Post.
"There's nothing going on." Another friend said: "Bruce and Patti are very much partners.
Springsteen's love life was last in the headlines in the late 1980s, when he began his affair with Scialfa - she was one of his backing musicians on tour - while he was still married.
It led to the breakdown of his relationship with his first wife, model Julianne Phillips, after four years.
Karen Darvin (1975) Model Karen Darvin was on the Boss' arm in the 1970s, frequently joining him on tour.
Since then, his work has become increasingly introspective and he is regarded as an elder statesman of American music.
Scialfa accompanied her husband for live performances this year and was in his band when he played in London to promote his latest album We Shall Overcome: The Seeger Sessions.
Yesterday, all members of Springsteen's entourage were under strict orders to say nothing about the reports, which surfaced in the New York Post.
"Bruce and Patti are separated but everyone has been sworn to secrecy," said a "friend" of the couple, who have three children - teenagers Evan and Jessica Rae, and their youngest, Sam.
She later had a relationship with musician Todd Rundgren.