The 38-year-old actor has said sorry "with a heavy heart" for the "tasteless comment" he made while speaking about the HBO fantasy series, in which he starred as Khal Drogo, on a Comic-Con panel in 2011, after a clip resurfaced online.
Speaking about switching between sci-fi and fantasy genres at the event, he said at the time: "But as far as sci-fi and fantasy, I love that genre because there are so many things you can do, like rip someone's tongue out of their throat and get away with it, and rape beautiful women."
But Jason — whose character Khal raped Daenerys Targaryen, played by Emilia Clarke, in the show — is now apologetic about the remarks.
He wrote on Instagram: "I awoke in Australia to the justified reactions by many people to a distasteful joke I made years ago in Hall H for which I am sorry. I am still severely disappointed in myself at the insensitivity of my remarks to that day.
"I know my sincerest apology now won't take away those hurtful words. Rape and sexual harassment can reach anyone and I have seen first hand its painful torment among members of my own family and friends.
"I made a truly tasteless comment. It is unacceptable and I sincerely apologize with a heavy heart for the words I said. All apologies, Jason. (sic)"
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Jason's comment was greeted with laughter by many of the Comic-Con crowd but a few of his co-stars were seen putting their hands to their faces.
The 'Batman v Superman: Dawn of Justice' star previously described shooting the uncomfortable scene.
He said: "Yeah, I'm raping Emilia. I love her, but I'm hurting her and she's crying. We could have made it longer, but you get the idea. I'm not a rapist! I prefer my women to enjoy sex."