The Dhaka University authorities rejected the BRAC University teacher's family permission to take his body to the Shaheed Minar on Wednesday.
Opposition BNP claimed Karim's family was denied permission as the government was against it.
Widely criticised for his comments on the Shahbagh-based mass movement and trials of suspected war criminals and dubbed an "agent of Jamaat-e-Islami" by many, Karim died of a cardiac arrest on Oct 13.
Protests erupted on Bangladesh's social media after his family announced plans to take his body to the Shaheed Minar. Various organisations threatened to thwart the move.
Agitators began gathering at the Shaheed Minar from Friday morning. They protested against the initiative to take Karim's body there.
Ruling Awami League's student front Bangladesh Chhatra League activists, too, went there to express solidarity with the protesters.
Piash Karim's body was taken to his Dhanmondi residence on Friday morning from the Square Hospital morgue.
It was taken to the Baitul Mukarram national mosque around noon where a funeral prayer would be held after Jumma prayers.
He will be buried at the Banani Graveyard, his family said.