Chowdhury's wife, Farhat Quader Chowdhury, told reporters immediately after the verdict that her husband would appeal.
"We will do whatever we need to do to show the world that this is a farce," she said.
Bangladesh says Pakistani soldiers, aided by local collaborators, killed 3 million people and raped 200,000 women during the nine month war that ended in December 1971. Prime Minister Sheikh Hasina set up the tribunal in 2010 to punish the alleged collaborators.
The opposition, led by former Prime Minister Khaleda Zia, has criticized the trials as an attempt to weaken the Bangladesh Nationalist Party and its allies.
Six people have already been convicted of war crimes by the tribunal. Four of them are currently top officials of the country's main Islamic party, Jamaat-e-Islami, while one is a former party chief and another is an expelled member of the party. Those verdicts led to widespread violence.
Jamaat-e-islami is the main political ally of Zia's party and is seeking to contest in next general elections under a Zia-led alliance. Jamaat-e-Islami shared two posts in the Cabinet during Zia's latest premiership in 2001-2006.
New York-based Human Rights Watch criticized the conduct of the tribunals, saying they are not up to international standards.
Hasina's government denies that the tribunal is biased. It points out that it pledged before the 2008 elections to prosecute those responsible for war crimes and that its 14-party political alliance won that election with a two-thirds majority.