Arafat Rahman Koko was buried at the Banani graveyard after the 'Namaz-e-Janaza' or the funeral prayers that were attended by thousands of people.
Zia gave her younger son an emotional send off touching his face in the coffin.
The funeral prayer was held at the Baitul Mokarram National Mosque.
Earlier, senior leaders of former premier Zia's Bangladesh Nationalist Party (BNP) received the body of Koko who died aged 45 on Saturday following a cardiac arrest.
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Koko's body was driven straight to her mother's Gulshan office from where she is spearheading a fierce campaign against Prime Minister Sheikh Hasina's government.
A large crowd had gathered in front of Zia's office awaiting the body.
The death of Zia's son came amid a BNP-enforced nationwide blockade which entered its 22nd day today.
Sporadic violence was reported and two more people died overnight to take the death toll in the violence to 37 with nearly half of them killed in arson attacks on buses and other public transport vehicles.
At least 37 people have been killed in violence during anti-government protests that took place following BNP's call for a nationwide non-stop blockade from January 6 after authorities barred its chief Zia from joining a protest rally to mark the first anniversary of the last year's divisive January 5 polls.
Senior BNP leaders, on condition of anonymity, said they plan to request Zia to invite Hasina to attend Koko's 'Qulkhwani' -- the Quran recitation and prayers for the deceased -- later this week.
"We will request madam (Zia) to invite the Prime Minister (Hasina) to attend the Qulkhwani but the decision will be taken by her," a BNP leader was quoted as saying by the Dhaka Tribune.