The 53-year-old musician recounts their dating history in his new memoir, "Then It Fell Apart", in which he claims the "Black Swan" star flirted with him in his dressing room after a concert two decades ago.
The singer alleges they began a romantic dalliance, but Portman broke off the budding relationship after meeting another man.
Portman challenged Moby's version of events in a new interview with Harper's Bazaar, arguing their friendship was strictly platonic on her part, until she realised he was "a much older man being creepy with me when I just had graduated high school."
Now Moby is fighting back by sharing an old photo of the pair on Instagram, in which he is featured pulling a wide, goofy smile while posing shirtless, with his arm around the actress' shoulders.
"I recently read a gossip piece wherein Natalie Portman said that we'd never dated," he captioned the image. "This confused me, as we did, in fact, date. And after briefly dating in 1999 we remained friends for years."
He went on to insist he respects her "intelligence and activism," but is puzzled as to why she would "actively misrepresent the truth about our(albeit brief)involvement (sic)."
Moby also takes issue with Portman's remarks blasting publishing executives at Faber and Faber for failing to fact check his stories prior to its release earlier this month.
"The story as laid out in my book Then It Fell Apart is accurate, with lots of corroborating photo evidence, etc.," he continued.
Moby concludes the post by admitting he could understand if Portman simply regretted embarking on a romance with him, but to deny the relationship outright is simply inaccurate.
He added, "Ps I completely respect Natalie's possible regret in dating me (to be fair, I would probably regret dating me, too), but it doesn't alter the actual facts of our brief romantic history."