Bangladesh was the eastern wing of Pakistan until it gained independence in 1971.
A special Bangladeshi tribunal handed down death penalty to him amid a nationwide shutdown called by Jamaat.
"He (Delwar Hossain Sayedee) will be hanged by neck till he is dead," pronounced chairman of the three-judge International Crimes Tribunal Justice ATM Fazle Kabir.
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The verdict sent his supporters into the streets, where they clashed with police, attacked government offices and uprooted railway tracks in parts of the country. Protesters also set fire to dozens of houses belonging to pro-government supporters.
Delwar Hossain Sayeedi, leader of Jamaat-e-Islami
Police responded with bullets and tear gas. Police and witnesses said Friday that 42 people, including six policemen, had been killed.
The government said the security forces were put on high alert across the country as Jamaat and Sayedee's supporters planned more protests Friday.
An additional 10,000 paramilitary border guards were deployed to boost security, said the home ministry, which controls security forces.
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"Our troops were deployed in 15 troubled districts in aide of civil administration... BGB (Border Guard Bangladesh) has been kept alert so it could move immediately wherever they are required," BGB chief major General Aziz Ahmed told PTI.
A police spokesman, meanwhile, said law enforcement agencies were on high alert as Jamaat and Sayedee's supporters planned more protests today.
Authorities feared that the JI activists might launch attacks on mosques during the Friday prayers.
In a statement Friday, Jamaat asked its supporters to converge in the country's mosques to offer a special mass prayer for those killed during the violence.
Authorities fear that the mass prayer may turn into street protests. Sayedee, 73, was convicted on eight of the 20 charges against him.
His lawyer Abdur Razzak rejected the verdict as politically motivated. He said the defendant will appeal the verdict to the country's Supreme Court.
Know more about - Jamaat-e-Islami: Bangladesh's Pakistan party
Prosecutor Syed Haider Ali said he was satisfied with the verdict. "Justice has been done to those who lost their loved ones at the hands of Sayedee," he said.
Sayedee, a teacher at an Islamic seminary school when he allegedly committed the crimes, is the third JI politician to be convicted by the International Crimes Tribunal since the trial of war crimes suspects, mostly belonging to the Islamist group, began three years ago.
The 120-page verdict said the tribunal found valid eight of the 20 charges against the Islamist leader which included mass killing, arson, lootings and forcefully converting non-Muslims to Islam of which two of the charges earned him the highest death sentence.
Jamaat-e-Islami activists march with sticks in the street during a clash with police in Thakurgaon, north-west from Dhaka. AFP
The verdict came as a security blanket covered the capital Dhaka and other major cities after JI called a nationwide shutdown coinciding with the date of the judgement while thousands of youngsters enforced a street vigil demanding the capital punishment for the war criminals.
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Sayedee, the Nayeb-e-Amir of JI, was arrested on June 29, 2010 and was indicted on October 3, for 20 charges of crimes against humanity including looting, killing, arson, rape and forcefully converting non-Muslims to Islam.
A total of 27 witnesses testified against him during the trial while Sayeedi's counsels brought 17 people to speak to defend their client.
Jamaat, the largest Islamic party in Bangladesh, campaigned against Bangladesh's independence, but denies it was behind any atrocities.
Jamaat is an ally of the country's main opposition Bangladesh Nationalist Party led by ex-Premier Khaleda Zia and was a partner in her government during 2001-2006.
Bangladesh says the 1971 war left 3 million people dead, 200,000 women raped and forced millions to take shelter in neighboring India.