Bhowmik went missing after he left his home in north-western Rangpur district on early Friday morning.
When the 58-year-old lawyer did not return home and his mobile phone was found switched off, his family reported about his disappearance to police and the Hindu community leaders.
His disappearance came a fortnight after seven terrorists from the Jamaat-ul Mujahideen Bangladesh were sentenced to death for murdering the caretaker of a Sufi shrine in November 2015.
Bhowmik led the case that saw nearly a dozen hardliners from the homegrown terrorist group convicted for killing the caretaker because they considered him a heretic.
A leading cultural activist, Bhowmik also lead the state's prosecution against five JMB extremists sentenced to death for the murder of 66-year-old Japanese farmer Hoshi Kunio in 2015.
"Their confessional statements led us to the dead body from an under construction building near Bhowmik's own house," said Benazir Ahmed, Director General of police anti-crime Rapid Action Battalion told news agency PTI.
He added that the lawyer's wife, a school teacher, and one of her arrested colleagues were directly involved in the murder pointing figure to their extramarital relations.
Police said the mobile phone records gave them the clue to the murder leading to his wife's arrest.
Police earlier launched a massive campaign amid huge protests to trace out Bhowmik suspecting militant links to his disappearance.
Rangpur regional police chief Khandaker Golam Faruque told AFP that Bhowmik had refused the offer of an armed escort during the high-profile trials.
"There was no threat against him. His family filed a complaint about his disappearance on Friday night," Mr Faruque said.
Bhowmik was also a crucial witness to the trial of senior Jamaate-Islami leader ATM Azharul Islam who was eventually sentenced to death by a special tribunal for committing crimes against humanity siding with the Pakistani troops during Bangladesh's 1971 Liberation War.
(With inputs from AFP and PTI)