Despite the protests of conservative Christians and warnings by state censors, Lady Gaga declared “I’m not a creature of your government, Manila”.
She then belted out her controversial song “Judas”, which her Filipino critics have labelled as blasphemous.
The audience tweeted photos of the US pop phenomenon wearing a full-length yellow dress inspired by Philippine national costume as she and a dance crew gyrated for the song “Born This Way” - a gay anthem.
The city government had earlier warned that her second show tonight could be banned if the censors among the audience monitored any hints of blasphemy, devil worship, nudity or lewd conduct.
Up to 40,000 fans in the Catholic-majority nation paid as much as 15,840 pesos ($372) each to watch the US singer.
Her world tour, “The Born This Way Ball”, has been dogged by controversy in Asia, with an upcoming concert in Muslim-majority Indonesia cancelled on police orders for fear of violence from religious hardliners.
In the Philippines, Catholic leader Archbishop Ramon Arguelles urged the public to boycott her two concerts. “Her fans are in danger of falling into the clutches of Satan,” he told reporters.
Former Manila mayor Lito Atienza, one of those calling for a concert ban, said he was opposed to the song “Judas”.
“We respect freedom of expression in this country. We also appreciate art and culture… but the laws should be respected,” he said.
But officials in the Manila district of Pasay allowed the show to go on last night at the Arena, a new, oblong theatre built in Pasay by the country’s richest man, Henry Sy of the SM shopping mall chain.
About 100 “little monsters” - the name given to Lady Gaga’s devoted followers - had lined up hours before the show, sporting her signature outrageous clothing, hairstyle and makeup.
A group of about 500 Christian activists tried to march on the Arena, singing religious songs while carrying placards saying “Stop Lady Gaga, the mother monster”.
However riot police stopped them about one kilometre away.
Local authorities earlier said they had worked out a deal to permit the show while addressing the clamour by Christian conservatives.
Censors were in the audience to monitor possible violations of a law against “immoral doctrines, obscene publications and exhibitions and indecent shows”, said Glenn Agranzamendez, secretary to Pasay mayor Tony Calixto.
Christian groups have vowed to send their own monitors and warned they could sue Lady Gaga under a law that penalises taking part or sponsoring “indecent shows” with prison terms of up to six years.
Lady Gaga’s concert in Indonesia was banned after Muslim groups vowed to start a violent protest,if she was granted permission to perform in the country.