Bedecked with medal ribbons on his green fatigues and wearing a four-star general's cap, Waker said 76-year-old Hasina had quit and that the army would "form an interim government".
"I give you my word that all the injustices will be addressed," the career infantry officer said in a broadcast to the nation on state television, although it was not immediately clear if he would head the new government.
"The country has suffered a lot, the economy has been hit, many people have been killed -- it is time to stop the violence."
The mild-looking, bespectacled officer was appointed as chief of army staff, the military's top job, only in June. Hasina had trusted him because he was a distant relative.
The experienced soldier has served as a UN peacekeeper as well as in Hasina's office.
His father-in-law was army chief during the first of Hasina's five terms as prime minister from 1996-2001.
The military declared an emergency in January 2007 after widespread political unrest and installed a caretaker government for two years.
Hasina then ruled Bangladesh from 2009 and won her fourth consecutive election in January after a vote without genuine opposition.
- 'Forge a beautiful future' -
As protesters stormed Hasina's palace on Monday and she fled by helicopter, Waker said he would speak to the president to form a government.
He vowed that the new authorities would "prosecute all murders" following weeks of deadly protests.
The army was deployed on the streets to crush the protests last month but shifted on Sunday and in several instances allowed demonstrations to go on.
Waker said he had held talks with the main opposition parties and civil society members, although not with Hasina's Awami League.
"All of us together will forge a beautiful future," he said. "If we work together, we can achieve a favourable outcome".
The Bangladesh Military Academy graduate, who served two tours as a UN peacekeeper in Angola and Liberia, called for the weeks of protests to stop.
At least 300 people were killed in the unrest.
"If the situation gets better, there is no need for emergency," he said.
Waker appealed to the university students who first launched protests in early July to support the army. The protests were initially against government hiring rules but spiralled into demands for Hasina to leave office.
"Now the task of the students is to keep calm and help us," he said.
Waker, who Bangladeshi media say is aged 57 or 58, also received officer training in Britain.
Married with two daughters, he holds master's degrees in defence studies from Bangladesh's National University and King's College London.
He was commissioned in 1985, also serving as an instructor at the army's college for infantry and tactics and at Bangladesh's institute for peace support operations.
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