Fundamentalist Jamaat-e-Islami Secretary-General Ali Ahsan Mohammad Mujahid, 67, and BNP leader Salahuddin Quader Chowdhury, 66, were hanged at Dhaka Central Jail at 12.45 AM, a senior jail official who witnessed the execution told PTI.
With Mujahid and Chowdhury's execution, Bangladesh has hanged four war crimes convicts so far.
Jail sources said a seven-member team of hangmen comprising prison inmates carried out the executions.
President Abdul Hamid rejected the mercy petitions of the two top opposition leaders, hours after they had sought presidential clemency in a last-ditch attempt to escape the gallows.
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The prison authorities had called the close relatives of Chowdhury and Mujaheed to see them for the last time.
Bangladesh is on high alert and a huge contingent of security forces has been deployed around the prison.
Paramilitary Border Guard Bangladesh (BGB), elite anti-crime Rapid Action Battalion (RAB), armed police and jail guards erected a several-tier security system stopping vehicular movements in thoroughfares around the prison complex.
On Wednesday, Bangladesh's Supreme Court upheld the death sentences against Chowdhury and Mujahid, who were convicted in 2013 on charges including genocide, rape and torture during the war.
Chowdhury, a top aide to BNP chief Khaleda Zia, carried out atrocities at his home district of southeastern Chittagong, leading a violent campaign against the Hindus.