APHR said the ruling could embolden religious hard-liners in the country and called into further question Indonesia's harsh Blasphemy Law, which permits prison sentences of up to five years for those found guilty.
Indonesia, 90 percent of whose 255 million people are Muslim, has a long tradition of pluralistic values and is home to substantial populations of Christians, Muslims and Buddhists.
Ahok was detained immediately after the verdict and taken to Cipinang detention facility in East Jakarta. Outside the court, his supporters wept at the news amid jubilant cheers from conservative Islamic groups.
The conviction and imprisonment of Jakarta Governor Basuki Tjahaja Purnama, better known as "Ahok", will tarnish Indonesia's reputation for tolerance, Amnesty International said today.More news: UP: Start here for our comprehensive coverage of the federal budget
Purnama, Jakarta's first non-Muslim governor for half a century and its first ethnic Chinese leader, looked calm when the verdict was announced and said he would appeal, as some of his supporters in court burst into tears.
Outside the court, hundreds of Islamic radicals wearing white Muslim skullcaps celebrated as they heard about the jail sentence.
Ahok rose from deputy governor in 2014 after Jokowi vacated the capital's governorship following his victory in Indonesia's presidential election that year.
The court's decision comes as a surprise to many, given prosecutors had only called for downgraded charges and the much lighter punishment of a year's suspended sentence on charges of hate speech.More news: Kane urges Spurs to finish games off after Chelsea defeat
The governor was charged with blasphemy after he made comments last September about the Al Maidah 51 verse of the Quran, regarding whether Muslims can elect a leader of another religion. Before the blasphemy controversy erupted, Purnama enjoyed a large lead in opinion polls due to his determination to clean up traffic-clogged, polluted Jakarta.
The verdict was met with strong protest.
Supporters of Jakarta Governor Basuki "Ahok" Tjahaja Purnama display a poster that reads "Free Ahok" during a rally outside the court where his sentencing hearing is held in Jakarta, Indonesia, Tuesday, May 9, 2017. "That's your right. If ladies and gentlemen feel that they should not vote because of fear of going to hell, being manipulated like that, it's okay", Ahok said in October.
An incorrectly subtitled video of his comments later went viral, helping spark huge demonstrations that ultimately resulted in him being bought to trial. "We want to see the blasphemer of Islam in jail". The legislation was rarely used during the 32-year rule of strongman Suharto, but in recent years it has been exploited to persecute minorities, rights groups say.More news: Messi, Suarez and Neymar combine to down Villarreal