Two ambulances, including one carrying the corpse of the Jamaat-e-Islami chief, reached his village around 6:15am on Wednesday.
His son Nazib Momen received the body from Upazila executive officer around 6:40am.
He was buried shortly after a funeral prayer.
Orchestrator of the murders of intellectuals just before the victory of Bangladesh, Nizami was hanged in the first hour.
Before the execution, Home Minister Asaduzzaman Khan Kamal said the war criminal had not pleaded for presidential pardon.
His relatives saw him for the last time at the jail on Tuesday evening. Preparation had been going at Santhia for the burial of Nizami who lived at Dhaka’s Banani with family.
Police had said the vehicles would go to Pabna via Farmgate and Uttara in Dhaka, Tangail, Bangabandhu Bridge on the Jamuna River, and Sirajganj.
Security had been beefed up in Gazipur, Tangail, Sirajganj, and Pabna.
Locals said Santhia was tense with law enforcers patrolling the area.
Santhia police OC Nasir Uddin told bdnews24.com that cleaning of the graveyard began after Tuesday evening.
Nizami’s cousin Abdullah Al Mamun said police had designated the place for his burial.
The 73-year old had exhausted all options to get his death penalty overturned, which was handed down by the International Crimes Tribunal (ICT) in 2014.
The legal battle that he waged even since his arrest on Jun 29, 2010, has been long.
He sought a review after the Supreme Court upheld the maximum sentence on Jan 6 this year but the petition was dismissed last week for having ‘no merit’.
But the home minister on Tuesday night said, “Nizami did not seek mercy. The executive order to carry out the death sentence has been sent to the prison authorities.”
Nizami was moved to Dhaka Central Jail from Kashimpur prison in Gazipur after his review petition had been thrown out and the final Appellate Division verdict was read out to him on Monday.