He is the governor of Indonesia's largest city, an ally of the president.
Basuki Tjahaja Purnama, also known as Ahok, was accused of insulting Islam by referring to a verse in the Koran in a campaign speech a year ago.
Nearly five months after the case began, a five-judge bench found the 50-year-old had deliberately committed blasphemy and hence was guilty of the charge.
Television footage showed an armored police van arriving at the prison on Tuesday and journalists waiting for Ahok to emerge.
Ahok and Djarot's term as governor and vice governor ends in October 2017.
Who is Jakarta's outgoing governor?
An Indonesian court has found Jakarta's Christian governor Basuki "Ahok" Tjahaja Purnama guilty of blasphemy against Islam and sentenced him to two years in jail, a judge said on Tuesday.
Hardline Islamist groups had called for the maximum penalty possible over comments by Purnama that they said were insulting to the Islamic holy book, the Koran.
Around 15,000 security personnel from the police and military are providing security at the scene, with riot police and armoured vehicles separating the rival groups. A few weeks later, roughly 200,000 conservative Muslims rallied in the Indonesian capital to protest Purnama, who is known as "Ahok" by his supporters. Some hugged each other. And the verdict is perceived as politically motivated. But a short distance away, the atmosphere among the governor's critics - a coalition of Islamic groups - was one of anger. Prosecutors had recommended a two-year suspended prison sentence.
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And that he be placed on probation for two years, rather than jailed.
Ahok was said to have made blasphemy comments during a pre-election speech last September.
In a video, the governor, also known as "Ahok", tells voters to reject an interpretation of a Koranic verse that purportedly prohibits Muslims from voting for a non-Muslim.
Purnama, also known by his Chinese name Ahok, was hauled into court past year to face trial for remarks he made in September 2016 while campaigning for re-election.
Ahok was widely praised for his work in tackling Jakarta's snarled traffic and chronic urban flooding, since replacing his predecessor, now-President Joko "Jokowi" Widodo in 2014.
The minority Christian governor is now on trial on accusation of blasphemy following his remark about a passage in the Quran that could be interpreted as prohibiting Muslims from accepting non-Muslims as leaders. This was viewed as a significant development for religious minority groups, especially given the violent anti-Chinese riots that occurred in 1998.
But the controversy overshadowed scheduled elections last month.
Indonesia is the world's most populous Muslim country.