"It seems so ridiculous I could be with my partner for 17 years and we have a son, and my partner and I can't get married," Sir Elton, 63, said during the 90-minute set in which he banged out Your Song, Sixty Years On, Levon and other hits he wrote before he came out as gay.
Sir Elton disappointed some gay activists after the California ban, known as Proposition 8, passed in 2008 when he said he had no desire to get married and was satisfied with the civil partnership he and his long-time partner, David Furnish, had.
"If gay people want to get married, or get together, they should have a civil partnership. The word 'marriage' I think, puts a lot of people off," he said at the time.
But Sir Elton was singing a different tune at the concert, which raised three million dollars for the American Foundation for Equal Rights.
He praised the effort to overturn the ban and promised to do everything he could to support it.
"As a gay man I think I have it all," he said. "I have a wonderful career, a wonderful life. I have my health, I have a partner of 17 years and I have a son.
"And you know what, I don't have everything, because I don't have the respect of people like the church, and people like politicians who tell me that I am not worthy or that I am 'less than' because I am gay."
He then punctuated his remark with an expletive, to cheers and applause from the crowd.
Furnish and Sir Elton became parents to a baby boy on Christmas Day. Their son, Zachary Jackson Levon Furnish-John, was born in California through a surrogate mother.