A message sent by Epstein, who is alleged to have taken the photo, reads: "Yes, she [Giuffre] was on my plane and yes, she had her photo taken with Andrew."
Epstein's statement appears to contradict the former prince's claim that he never met Ms. Giuffre and also refutes her long-standing claim that the photo of him with his arm around her neck may have been doctored.
This email, dated July 2011, was published on Wednesday along with more than 20,000 pages of correspondence from the convicted sex offender and disgraced financier's estate.
Ms. Giuffre, a key accuser of Epstein, alleged that Andrew had sex with her three times when they were teenagers.
Andrew, who has denied the allegations, reached an out-of-court settlement with Ms. Giuffre in 2022. It contained neither an admission of responsibility nor an apology.
The email, sent by Epstein to his publicist, Peggy Siegal, was sent shortly after Ms. Giuffre was publicly identified in the Mail on Sunday.
The newspaper also published a photo of Andrew with Ghislaine Maxwell, who is currently serving a 20-year prison sentence for sex trafficking.
Epstein's message contradicts claims made by Andrew in a 2019 Newsnight interview, in which he denied meeting Ms. Giuffre and suggested that the photo—or parts of it—may be fake.
Andrew said at the time: "No one can prove whether that photo has been doctored, but I don't recall that photo ever being taken."
Documents published by Democrats to the House Oversight Committee also reveal that Andrew and Epstein remained in contact four months after the prince claimed their relationship had ended.
It appears that on March 4, 2011, Maxwell sent a reply-to email from the Mail on Sunday to Epstein.
It mentions several allegations, including that Andrew had sex with a young woman he had introduced to him at Maxwell's London home in 2001.
It appears that Epstein sent this message to Andrew through a redacted email address under the name "The Duke."
Andrew's response reads: "Please ensure that every statement or legal letter clearly states that I am not involved and that I did not and do not know anything about these allegations. I cannot tolerate this any longer."
The Mail on Sunday published its story with a photo.
This included allegations that the girls were asked to sit on Andrew's knee at Epstein's New York home, that he touched them, and that they had sex on Epstein's private island.
The documents also reveal Epstein's attempts to discredit Ms. Giuffre's testimony.
In a July 2011 email to his publicist, Epstein also wrote: "The girl who accused Prince Andrew could easily be proven a liar. I think Buckingham Palace would love that."
"You should assign someone to investigate Virginia Roberts, the girl who has caused so much distress to the Queen's son."
This latest release comes after Democrats in the US Congress urged Andrew to answer questions regarding the Epstein investigation. Epstein died in prison in 2019 while awaiting trial for sex trafficking offenses.
Congressman Suhas Subramanian, a Democrat on the House Oversight Committee, told BBC Newsnight that Andrew has not yet responded to the committee's invitation to testify before the committee.
He said the former prince "doesn't need to board a plane to testify; he can testify remotely."
Earlier this month, Andrew was stripped of all his titles after Ms. Giuffre's posthumous memoir reignited interest in his relationship with Epstein and Maxwell.