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In April, prosecutors had called for the blasphemy counts to be dropped in exchange for a lesser charge of "spreading hate," but the judges appear to have ignored that recommendation.
The controversial Chinese Christian politician was put on trial in December over accusations that he insulted Islam while campaigning for re-election. He repeatedly denied the charges.
The Jakarta governor sparked controversy in late 2016 after quoting a verse from the Quran to prove to his supporters that there were no restrictions on Muslims voting for a non-Muslim politician.
Almost no one who has been charged under the blasphemy law has ever escaped conviction, associate professor of Indonesian politics at the Australian National University Greg Fealy told CNN.
"The blasphemy law has really been a blight on the rule of law and democracy in Indonesia for decades," he said, adding that "the fact that Ahok was charged at all was really a product of massive street demonstrations that frightened the government into acting."
Growing conservatism
While Indonesia has built a reputation as a tolerant, diverse nation, experts say Ahok's conviction is the latest example of the country's growing conservatism.
Recent years have seen large anti-LGBT protests in Jakarta in early 2016, a push to criminalize homosexual sex and passionate reactions to allegations of blasphemy.
A blow for religious tolerance
As well as being a minority ethnic Chinese Indonesian, the outgoing governor is also a Christian.
He was defeated by former Indonesian education and culture minister Anies Baswedan, a Muslim, after a campaign riven by religious tensions.
On the day of the election, the Jakarta Post editorial board described the campaign as the "dirtiest, most polarizing and divisive" ever seen in Indonesia.
Fealy said Ahok's conviction was a blow for religious tolerance in Indonesia.
"We must acknowledge that Ahok was always a special case ... (but) if you were a non-Muslim and you were considering a career in public life, you're probably more likely to think twice about that," he said.