TV channels showed an ambulance entering the jail after its huge iron gates were opened, presumably to carry Mollah's body to his village in western Faridpur.
Dhaka's district magistrate, civil surgeon and prison officials witnessed the execution in line with rules while an Islamic cleric administered a special prayer when Mollah sought God's mercy while taking his last bath.
Paramilitary Border Guard Bangladesh (BGB), elite Rapid Action Battalion (RAB) and riot police formed a three-tier security blanket as the Jamaat had earlier warned of dire consequence if its assistant secretary general was executed.
Witnesses said Mollah's two sons, four daughters and wife were his last visitors at around 6:25pm.
Mollah, the fourth-highest Jamaat leader, was the first war crimes convict to be sent to the gallows since Bangladesh's independence in 1971.
The apex court earlier today rejected Mollah's petition for a review of his death sentence, removing the last barrier for his hanging two days after his execution was dramatically put on hold in a last-minute reprieve.
Jail officials earlier in the day said Mollah refused to seek presidential clemency under a constitutional provision despite being approached thrice.
Mollah sided with Pakistani troops during the war and gained notoriety for leading the infamous Al-Badr militia in the Dhaka suburb of Mirpur, where he had a role in slaughtering a large number of people, including women and children.