Purnama, who is on trial for blasphemy, topped the first round with 43 percent and will go head-to-head with Anies Baswedan who came second with 40 percent.
Stakes in the vote have been raised by allegations that Purnama — the city’s first non-Muslim governor for half a century and its first ethnic Chinese leader — insulted the Koran.
The claims drew hundreds of thousands of conservative Muslims onto the streets of Jakarta in major protests last year, but the case has been criticised as unfair and politically motivated.
Purnama will face former education minister Baswedan on April 19.
Jakarta election commission head Sumarno, who goes by one name, said a run-off would be held because no candidate “reached more than 50 percent of votes”.
Agus Yudhoyono, the son of the former president, trailed the first round with just 17% and must now drop out.