Human rights organisations condemned the sentencing as a setback for human rights and said it could worsen discrimination against people in Malaysia's LGBT community.
Women's Aid Organisation said it was "appalled by this grave violation of human rights".
Amnesty International Malaysia said in a statement: "Caning is a form of cruel, inhuman and degrading treatment and may amount to torture.
"People should not live in fear because they are attracted to people of the same sex. The Malaysian authorities must immediately repeal repressive laws, outlaw torturous punishments and ratify the UN Convention Against Torture."
Muslim Lawyers' Association deputy president Abdul Rahim Sinwan told AP that, unlike caning under civil laws, the punishment under Islamic laws isn't painful or harsh and was meant to educate the women so they will repent. The women, dressed in white headscarves and clothing, didn't cry or scream but "showed remorse," he said.
"Repentance is the ultimate aim for their sin," he added.
Malaysia follows a dual-track justice system. Nearly two-thirds of Malaysia's 31 million people are Muslims, who are governed by Islamic courts in family, marriage and personal issues.
Malaysia is seen as a moderate and stable Muslim-majority country, but Islamic conservatism is on the rise.
The caning occurred amid a climate of fear and discrimination against Malaysia's LGBT community. A few weeks ago, authorities removed the portraits of two LGBT rights activists from a public exhibition. Malaysia religious minister Mujahid Yusuf later said the Government doesn't support the promotion of LGBT culture.
A transgender woman was also beaten up by a group of people in a southern state.
- with AP
