"Her majesty celebrated our good times and she stood with us during trials and hardships, happy and glorious," Mr Albanese said in a televised address on Friday morning following news of the 96-year-old monarch's death.
In the coming days the prime minister will travel to London with Governor-General David Hurley to convey the sorrow of Australians.
Queen Elizabeth visited Australia 16 times during her reign, visiting every state and territory.
During her first visit to Australia in February 1954, 70 per cent of Australians turned out to catch a glimpse of the young Queen, Mr Albanese said.
"Throughout her reign Queen Elizabeth II showed her deep affection for our country," he said.
"As she said at the Sydney Opera House in the year 2000 'since I stepped ashore here, I have felt part of this rugged, honest, creative land and I have shared in the joys and sorrows, the challenges and the changes that have shaped this country's history.'
"Her Majesty celebrated our good times, and she stood with us during trials and hardships, happy and glorious but steadfast too.
"In particular we recall the sympathy and personal kindness she extended to Australians afflicted by tragedy and disaster from floods and bushfires."
Queen Elizabeth II was the only reigning monarch many had known and the only one to visit Australia, the prime minister said.
"Today marks the end of an era the close of the second Elizabeth's age.
"This time of mourning will pass but the deep respect and warmth regarding which Australians have always held for Her Majesty will never fade."
Opposition Leader Peter Dutton said the "last page has been inked on an exceptional reign".
"A Monarch who ruled with an empathetic heart and wisdom both innate and gained from almost a century of life and experience," he said of the Queen.
"Her Majesty was gentle, kind, and much-loved."
Mr Albanese and Governor-General David Hurley are expected to travel to London for the Queen's funeral.
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