The bill, which in its original form prescribed the death penalty for cases of "aggravated homosexuality" -- for instance if someone is infected with HIV -- reduced the penalty to life imprisonment before the vote.
Clauses that criminalize the "promotion" of homosexuality could cause activists and even doctors treating gay patients with HIV to face prison time.
The United States opposes "any legislation that undermines a person's enjoyment of his or her human rights, and for that reason we condemn legislation that criminalizes consensual sexual conduct between adults or criminalizes simply being of a particular sexual orientation or gender identity," a State Department official said
Emphasizing that Washington respects Uganda's sovereignty, the official noted that some of Uganda's own government institutions have spoken out "against further criminalization of homosexuality."
"As Americans, we believe that people everywhere deserve to live in freedom and equality -- and that no one should face violence or discrimination for who they are and whom they love," State Department spokeswoman Jen Psaki said.
"We join those in Uganda and around the world who appeal for respect for the human rights of LGBT persons and of all persons."
Among those condemning Uganda's anti-gay bill was British billionaire and Virgin chief Branson, who tweeted that he "wouldn't do business in Uganda due to their dreadful anti-gay laws." He urged others to follow suit.
In a statement on his website, under the headline "Let people love whoever they want," Branson wrote that he was seriously considering doing business in Uganda, but the "witch hunt against the gay community and lifetime sentences means it would be against my conscience to support this country."
"Governments must realise that people should be able to love whoever they want," he wrote. "It is not for any government (or anyone else) to ever make any judgments on people's sexuality. They should instead celebrate when people build loving relationships that strengthen society, no matter who they are."
Gay-rights activists have warned of mounting violence against homosexuals after Parliament passed the controversial legislation last week.
Homosexuality is illegal in most African countries, where sodomy laws were introduced during colonialism.
In Uganda, homosexual acts have been punishable by 14 years to life in prison, according to rights activists. But lawmakers in the conservative nation sought even harsher legislation, saying the Western lifestyle risks destroying Ugandan family units.
"What we are convinced and sure of is that nobody can in one's right conscience and consciousness choose to be homosexual," said Simon Lokodo, Uganda's minister for ethics and integrity. "This must be under pressure or conditions because we know that the natural tendency is always for a male to go for a female and vice versa."
For the bill to become law, President Yoweri Museveni will have to approve it within 30 days.