The Avengers star was seen staring blankly at photographers while John planted a peck on her cheek at the annual Academy Awards on Sunday night.
Her lack of smile in the photo led many to question whether she a) knew he was about to kiss her and b) liked it.
Now, Scarlett has cleared up the rumours, insisting she adores John and loved seeing him again at the awards show.
In a statement to The AP, she said: "There is nothing strange, creepy or inappropriate about John Travolta.
"The image that is circulating is an unfortunate still-frame from a live-action encounter that was very sweet and totally welcome
Meanwhile, a rep for John recently told People that he'd had a "great time" at the Oscars because he was there with actress wife Kelly Preston and their daughter Ella Bleu.
Scarlett and John were both presenters at the show.
John teamed up with 'Let It Go' singer Idina Menzel to announce the 'Best Original Song' winner, while Scarlett introduced the Sound of Music anniversary tribute by Lady Gaga.
Red carpet photos from The Oscars:
Copyright: Rex Features Jim Smeal/BEI
For exclusive competitions and amazing prizes visit Reveal's Facebook page NOW!