Pillay noted during a visit that the Maldives had progressed in safeguarding the rights of its 330,000 Sunni Muslims, but more needed to be done to protect women.
Flogging, carried out with a cane, is normally handed down as a punishment by village chiefs who also act as local judges.
Rights activists slammed the judgement and called for it to be overturned.
"Degrading and inhuman punishments should find no place in a democracy," said Aruna Kashyap, women's rights researcher for Asia at Human Rights Watch.
"Maldives should immediately halt the execution of the punishment and take action to amend its discriminatory laws."
Suhas Chakma, director of the Asian Centre for Human Rights, said the sentence reflected the government's intention to consolidate its support among sharia law followers, in the face of serious political opposition.
"This could be used by the government to say they're committed to Islam," he said. "Courts are not independent in the Maldives so the government will have a hand."
He said the lashes were also a breach of the UN Convention against Torture.
There were mixed reactions in comments posted on the local news website Minivan News.
"This is ridiculous, and hypocritical," said one reader, identified as Mariyam.
"How many people over the age of 18 are having sex outside of marriage every day in this country. Why not flog them. And why not flog the 29-year-old man. If the girl has to face public humiliation why not the man."
Another, identified as Dhivehi Hanguraama, volunteered to administer the lashing.
"I myself would volunteer to whip this creature, as would any of self-respecting, esteemed, members of the ulama (religious scholars)."
Police said they began their probe after receiving a complaint from the girl's family.
"We investigated and forwarded our findings to the prosecutor general. The man was convicted of having sex with a minor," police spokesman Hassan Haneef said.
Official sources said the girl had been tried under sharia law which prohibits girls between the ages of 13 and 18 having pre-marital sex. Sex with a girl under the age of 13 is considered rape.
She was convicted on the basis of her confession.
Her lover, on the other hand, was tried under common law and convicted of having sex with a minor, an offence punishable with a sentence of up to 15 years in prison.
The pair had intercourse on the Raa atoll, about 200 kilometres (125 miles) north of the capital island Male.
There was no immediate comment from the Maldivian government, which includes the ultra conservative Adhaalath Party, whose supporters follow a strict brand of Wahhabi Islam.
The country's first democratically elected president, the Western-educated Mohamed Nasheed, resigned in February saying he was forced out in a coup backed by Islamic extremists along with elements of the police and the armed forces.
The unnamed teenager was convicted on her confession under sharia law after her family complained she had sex with a 29-year-old man in July.
The man was given 10 years in jail during a court hearing on the remote Raa atoll on Sunday.
A court official said the girl could refuse the flogging and would then instead be subjected only to eight months house arrest. Should she agree, the lashing will be carried out when she reaches the age of 18.
"In most cases, the offenders would accept the lashing as part of penance," the official, who declined to be named, said.
