"My choice of words was regrettable, not because I do not believe Justice Thomas is deeply wrong, but because they were ad hominem and uncivil, and for that I am sorry," Takei wrote in a July 3 Facebook post.
Takei, who married his partner Brad in California in 2008, had taken issue with Thomas' dissenting opinion in the high court's landmark ruling on same-sex marriage.
"Slaves did not lose their dignity (any more than they lost their humanity) because the government allowed them to be enslaved," Thomas, who is black, wrote in his dissent. "The government cannot bestow dignity, and it cannot take it away."
During an interview with Fox 10 in Phoenix, the former Star Trek star described Thomas as a "clown in blackface sitting on the Supreme Court. He gets me that angry."
Takei, who has become a prominent social media user, wrote later to his 8 million Facebook followers that he was "seething" when he spoke to the news station.
"In my mind that suggested that this meant he felt the government therefore shouldn't be held accountable, or should do nothing in the face of gross violations of dignity," Takei said in his Facebook apology. "When asked by a reporter about the opinion, I was still seething, and I referred to him as a 'clown in blackface' to suggest that he had abdicated and abandoned his heritage."
"This was not intended to be racist, but rather to evoke a history of racism in the theatrical arts," Takei added. "While I continue to vehemently disagree with Justice Thomas, the words I chose, said in the heat of anger, were not carefully considered."