The assembly adopted a motion, unanimously supported by all parties, that called Morgentaler a lifelong champion of women's rights.
It also held a minute of silence and offered condolences to Morgentaler's family.
The motion was tabled by Premier Pauline Marois, who then gave a speech praising Morgentaler and she was followed by colleagues in other parties.
"A man of great stature, a humanist, has left us," said Marois, who added that even before taking up the abortion cause this "good and generous man" had served society as a family doctor for 20 years.
"Henry Morgentaler paid a heavy personal price for moving our society forward, for dignity, safety and the health of women. Henry Morgentaler was a great Quebecer — a historical figure we can be proud of."
No similar tribute is planned by the federal government, which declined to issue even an informal statement on the death Wednesday.
The federal Opposition leader isn't surprised by the lack of a reaction in Ottawa.
"The Conservatives have consistently tried to reopen the abortion debate. They keep finding new ways to do it," NDP Leader Tom Mulcair told a news scrum in Montreal.
"The NDP says this has been settled law in Canada for a long time and the departure of someone who fought so hard for women's rights in Canada is something worth marking."
He noted that NDP MP Nikki Ashton had spoken in the House of Commons about Morgentaler, crediting his courage and pursuit of equality. There was also a written tribute from Ontario's premier, with Kathleen Wynne calling Morgentaler a "man of great courage" who contrinuted to a fairer society.
In Quebec, where Morgentaler opened his first abortion clinic in 1969, abortion rights have especially enthusiastic political support and also have strong public support according to opinion polls.
Thursday's event led to a rarity in the Quebec legislature: an opposition member spoke briefly in English, in order to offer condolences to Morgentaler's family.
"An entire country and many generations of women will be eternally grateful to Dr. Henry Morgentaler, who offered them the most precious of gifts — the freedom to choose your own path in life," Liberal MNA Maryse Gaudreault said in French.
She then added, in English: "We would like to offer our sincere condolences to the Morgentaler family."
There was another rare moment when one opposition party leader, Francoise David of Quebec solidaire, praised the premier.
She thanked Marois and expressed doubt that too many other provincial premiers would be willing Thursday to deliver the kind of tribute she just had.
Morgentaler, who died the previous day in Toronto at age 90, began his abortion-rights movement in Montreal where he had lived for decades.
The motion in the Quebec legislature read as follows:
"That the national assembly notes the passing of the late Dr. Henry Morgentaler and salutes the memory of a great man, a defender of women's rights until the end of his life;
"That it recognizes his invaluable contribution to the achievement of a fundamental freedom for women: that of giving birth to children when they want, and as they want;
"That it thanks Dr. Morgentaler for leading with courage and determination this great social and political struggle, and...
"That it offers condolences to the family and friends of Dr. Morgentaler."
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