New South Wales Premier Barry O'Farrell admitted to a "massive memory fail" after telling a corruption inquiry that he never received the wine.
Mr O'Farrell said he could not remember calling businessman Nick Di Girolamo, who sent him the gift in 2011.
He acted after investigators unveiled a handwritten thank you note from him.
'No recollection'Mr O'Farrell, leader of the New South Wales Liberal Party, announced his resignation at a press conference in Sydney on Wednesday.
He told reporters that he "did not seek to mislead" the inquiry.
"I do accept there is a thank you note signed by me and as someone who believes in accountability, I accept the consequences of my action," he said.
He added that a new premier would be elected at a parliamentary meeting next week.
"I still cannot explain either the arrival of a gift that I have no recollection of, or its absence which I certainly still cannot fathom. But I accept the consequences in an orderly way."
Australian Prime Minister Tony Abbott, who leads the Liberal-National coalition, said Mr O'Farrell's resignation was a sign of integrity, not corruption.
"Obviously, as we now know, he innocently and inadvertently misled ICAC yesterday and has taken the utterly honourable step of resigning as premier," he said.
Opposition politician John Kaye said there was a broader lesson in Mr O'Farrell's announcement.
"This is not about Barry O'Farrell, it is about the culture of politics in New South Wales," he said.
"Barry O'Farrell was clearly inundated with gifts and donations with lobbyists but he just lost track of what was going on."
Mr O'Farrell received the bottle of 1959 Penfolds Grange Hermitage from businessman Nick Di Girolamo, whose company, Australia Water Holdings, is being investigated by the New South Wales corruption body.