The two men handed death sentences were named as Faisal bin Nayem and Rezwanul Azad Rana.
Rana, named the "mastermind" of the killing by local media
, remains on the run and was convicted in absentia, Farukh Hossain, superintendent of police, Dhaka tells CNN.
Mufti Jashimuddin Rahmani was given a five-year sentence for his role in the killing.
Haider was the first in a string of secular writers and publishers who have been murdered in Bangladesh. In total six have been killed since Haider was hacked to death
in the Mirpur section of the capital Dhaka in February 2013.
Imran Sarkar, the head of the Blogger and Online Activists Network, an advocacy group in Bangladesh, said that the group "boycotted" the verdict, arguing that the sentencing was too lenient for some of the accused.
"All of the accused are self-declared killers. There should have been capital punishment on all of them," he said.
"This is completely unacceptable."
Haider's father told CNN that he was "extremely sad and disappointed" over the verdict.
"They intentionally killed my son... I did not get the justice I expected."
Foreigners and Shia Muslims have been killed in Bangladesh this year, in attacks claimed by ISIS.
Those attacks included a September 28 killing of an Italian national, an October 3 killing of a Japanese national and October 24 bombings against Shia Muslims in a religious procession, according to the State Department.
The U.S. Embassy in Bangladesh warned U.S. citizens this week that attacks against hotels and clubs are possible in Dhaka in the next few days, perhaps in connection with New Year's Eve celebrations