The 42-year-old construction worker was given six lashes in Malaysia's conservative state of Terengganu after being convicted by a Sharia court, the official Bernama news agency said.
It was the first instance of a Sharia court-ordered whipping taking place outside of a court setting in Malaysia according to the agency.
An AFP journalist saw the man delivered to the mosque in a prison van after Friday prayers, wearing an orange inmate's jumpsuit as he entered before a hushed crowd.
The caning in punishment for the Islamic crime known as "khalwat" took place inside the mosque after an audience of around 90 people was admitted.
Earlier this week the Malaysian Bar association of lawyers said it had "profound concern" over the decision to flog the man.
"Such punishments strip individuals of their dignity," a statement said.
But Spectator Mohd Sabri Muhammad said he hoped the it would deter those "tempted to commit immoral acts".
"Valentine's Day, New Year's, there are many opportunities for young people to engage in inappropriate behavior," the 37-year-old told AFP.
Multi-ethnic Malaysia has a dual-track legal system, with Islamic courts handling some matters for Muslim citizens.
Caning typically takes place on a fully-clothed person and critics say it aims to humiliate as well as physically punish the recipient.
Sharia court-ordered caning is rare but not uncommon in Malaysia.
Two women convicted of violating religious laws by having sexual relations were caned in front of more than 100 spectators in an Islamic court in 2018.
The Human Rights Commission of Malaysia said last week that "punishments that inflict physical violence and public humiliation have no place in a modern justice system".
