She was taken to the Square Hospital on Friday morning, a day after the brutal attack, said Ahmedur Rashid Titu, owner of the publisher Shuddhaswar.
She was kept at the Intensive Care Unit (ICU) of the hospital, he added.
Bonya lost one of her fingers in the attack.
A bio-engineer and a naturalised US citizen, writer Avijit Roy was hacked to death near the TSC intersection at Dhaka University on Thursday.
Bonya was injured as she tried to protect Avijit.
Religious radicals had been threatening Avijit for his active campaign against Islamist extremism.
He was a regular bdnews24.com columnist and the founder of the popular blog, Mukto-Mona (Free-mind).