The 53-year-old musician recounted their alleged dating history in his book "Then It Fell Apart", in which he claimed the "Black Swan" star flirted with him in his dressing room after a concert two decades ago.
Portman later denied Moby's version of events in an interview with Harper's Bazaar, and argued 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".
The "Porcelain" hitmaker was adamant the pair had dated, but he's now backtracking in an apology to the mother-of-two.
In a post on Instagram on Saturday, May 25, Moby admitted it was "inconsiderate" of him not to reach out to Portman before publishing the book.
"As some time has passed I've realized that many of the criticisms levelled at me regarding my inclusion of Natalie in Then It Fell Apart are very valid," he wrote. "I also fully recognize (sic) that it was truly inconsiderate of me to not let her know about her inclusion in the book beforehand, and equally inconsiderate for me to not fully respect her reaction."
"I have a lot of admiration for Natalie, for her intelligence, creativity, and animal rights activism, and I hate that I might have caused her and her family distress."
He went on to offer his sincere apologies to everyone else he had included in his book without their knowledge.
"I tried to treat everyone I included in Then It Fell Apart with dignity and respect, but nonetheless it was truly inconsiderate for me to not let them know before the book was released," he continued.