“I know as a Christian that the Bible speaks against homosexuality, but I have taken an oath and I am very serious about my oath,” he told reporters in Johannesburg.
“It cannot be a lie when I assure the nation that I will uphold the Constitution, the laws and the human rights.”
Mogoeng pointed out the right to sexual orientation was a human right and it would be perverse of him not to accept that.
“Justice is not supposed to be perverted, to begin to get at those who are gay and lesbian just because of their choice.
“My responsibility is to ensure that every gay person, every lesbian person enjoys their right as protected by the bill of rights. There’s no question about that,” he said.
Mogoeng, who is a lay minister, has been criticised for his strong religious views.
He was defending a speech he gave in Stellenbosch last week about religion and the law. Mogoeng caused a stir by suggesting religion could be used to strengthen legislation and lead to a better society.
The chief justice said he would not allow his faith to take precedence over the Constitution.