He said: "During the course of the entire inaugural festivities, there are going to be a wide range of viewpoints that are presented.
"That's part of the magic of this country ... that we are diverse and noisy and opinionated"
"And that's how it should be, because that's what America is about. That's part of the magic of this country ... that we are diverse and noisy and opinionated."
Warren is known as an evangelical focused on fighting poverty and disease, including Aids in Africa, but he also advocated California Proposition 8, a ban on gay marriage that voters in the state backed last month.
"I commend President-elect Obama for his courage to willingly take enormous heat from his base by inviting someone like me, with whom he doesn't agree on every issue, to offer the invocation at his historic inaugural ceremony," Warren said in a statement on Thursday.
"Hopefully individuals passionately expressing opinions from the left and the right will recognise that both of us have shown a commitment to model civility in America."
'Second class citizenship'
Harry Knox, a gay rights campaigner from Human Rights Campaign, told Al Jazeera that the gay and lesbian community was "profoundly disappointed" at Obama for putting someone as "divisive and mean spirited" as Warren on the podium on an occasion meant to be inclusive of all American society.
"We all have biological predispositions ... I'm naturally inclined to have sex with every beautiful woman I see. But that doesn't mean it's the right thing to do"
Rick Warren, pastor, Saddleback church
He said Obama was foisting "second class citizenship" on the community with his decision.
And while saying that the group that strongly backed Obama during the election campaign was "not yet" withdrawing it support, he added: "We must say to him: you have really insulted us and we expect you to do better in the future."
In an interview with US broadcaster NBC news, Warren denied he was homophobic, saying the "hate speech against [him] is incendiary".
"I don't know any church in America that's done more to help the gay community, particularly with Aids, than Saddleback," he added.
Warren said he would not change his opposition to gay marriage even if homosexuality were scientifically proved to be a result of biological predisposition.
"No [I would not change my position] ... and the reason why is we all have biological predispositions," he said.
"I'm naturally inclined to have sex with every beautiful woman I see. But that doesn't mean it's the right thing to do."