Mr Emwazi appeared in a succession of grim online videos in which Western hostages are beheaded. The clip, with the caption "Rod Stewart (leader) band doing a "Beatles" sand dune crossing", was posted and later deleted by Stewart's model wife Penny Lancaster.
However, the singer claimed in a statement that Game of Thrones inspired the gag; the HBO series' notorious "Red Wedding" scene features similar throat-slicing, but not the kneeling or desert setting that the Jihadi John videos contained.
Stewart says the clip - which was shot before his tour stop in Abu Dhabi - was meant to be a Game Of Thrones reference and that fans are misinterpreting his intent.
72-year-old Rod issued an apology, saying they were "larking about pre-show" and were "spontaneously playing out Game Of Thrones".
Stewart was in the UAE capital of Abu Dhabi as he was performing at an arena concert.
On Twitter, Stewart apologized and said he and his friends were just "larking about" and the video was "understandably. misinterpreted".
Behind her, the singer stands behind and appears to put his hand across the neck of a friend, who is sitting in front of him.
Bethany said: "I had a lot of respect for Rod Stewart, now you couldn't pay me to listen to his music".
Stewart's next live performance will be at The Colosseum At Caesars in Las Vegas on March 15.