The sentence was handed down last month once the women, who are 32 and 22, had pleaded guilty after Sharia enforcement officials in the northeastern state of Terengganu found them having sex in a vehicle.
Muslim Lawyers' Association deputy president Abdul Rahim Sinwan said the women, aged 22 and 32, were given six strokes on their backs by female prison officers.
The case marks the first time two women have been sentenced for pursuing same-sex relations.
And it was also the first time the kind of punishment that was open to the public.
Satiful Bahri Mamat, an official in charge of Shariah implementation, said the caning serves as a public reminder to Muslims against committing illicit sex acts, which he called a "cancer that can spread in society", MalayMail reported. "Suhakam cautions the government that undermining Malaysia's global human rights obligations rather than to uphold them would not be in the best interest of progress and success", it added.
Amnesty International said the caning marked "an appalling day" for human rights in Malaysia.
The caning was witnessed by more than 100 people, according to local news outlet The Star.
Last month they pleaded guilty to attempting lesbian sex and were fined and sentenced to six lashings of the cane.
"This is a awful day for LGBTI rights, and indeed human rights, in Malaysia".
But Muslim Lawyers' Association deputy president Abdul Rahim Sinwan told the Associated Press that the punishment isn't painful and is created to educate the women so they repent. "Not only for LGBT people but all persons because corporal punishment affects all people".
Malaysia has a dual track legal system where sharia courts can handle religious and family matters. Satiful said the punishment was "not meant to torture or injure but to serve as a lesson to society".
KUALA LUMPUR, Sept 4 ― The Human Rights Commission of Malaysia (Suhakam) joined others in urging the government to end all forms of corporal punishments following the controversial caning of two women in Terengganu over same-sex relations.
It reads: "Homosexual acts are illegal in Malaysia and punishable under federal law, and in some states, shari'a law". "We really need to make sure that no one is publicly caned. due to their sexuality", he said. A transgender woman was also beaten up by a group of people in a southern state this month. Malaysia is seen as a moderate and stable Muslim-majority country, but there has been a shift toward increasingly conservative Islam in recent years.
Almost two-thirds of Malaysia's 31 million people are Muslims who are governed by Islamic courts in family, marriage and personal issues.