Cheers and applause went up from a crowd gathered outside a mosque in the city of Banda Aceh, capital of the conservative province of Aceh, as the masked men took turns to flog the pair on a raised platform.
The men stood quietly, their heads down, as spectators heckled them and shouted insults.
The punishment, condemned by rights groups, marked the first application of anti-homosexuality laws introduced in the province in 2014.
Aceh has long had a reputation as Indonesia's most conservative region. It is the only province that criminalises same-sex relations and that uses Islamic law as its legal code in addition to the national criminal code.
Up to 1,000 people, many filming with smartphones, watched as the two men received 82 lashes each. Many others watched the punishment being meted out on a livestream video.
Some in the crowd carried banners rejecting the presence of the lesbian, gay, bisexual and transgender (LGBT) community in Aceh.
"I hope there won't be any more such cases of homosexuality, it is shocking," said Eni Tri Retnaningsih, a 20-year-old student who said she had watched others caned before for other offences such as adultery.
At least eight other men and women were caned for other offences ahead of the punishment of the two found guilty of having gay sex.
Police separated men and women in the crowd as proceedings began, with 10 men in brown robes and hoods preparing a bundle of canes in case any broke during the flogging.
-Reuters