She is in Sydney ahead of the opening of the Commonwealth Games in Melbourne on Wednesday.
Enthusiastic onlookers and well-wishers gathered on the Opera House forecourt steps, waving Australian flags as the queen emerged from her car.
She was greeted by Australian Prime Minister John Howard, Governor-General Michael Jeffery and New South Wales governor Marie Bashir.
Canon fire was heard as she mounted a special podium beneath the Commonwealth flag, while the Royal Australian air force performed the national anthems of Australia and Britain.
Inside the Opera House, she paid tribute to the building's architect Joern Utzon, and said it is fitting the building is being considered for world heritage listing.
"The first time I came here on a glorious summer's day 52 years ago there was of course no Opera House," she said.
"The city was smaller, the skyline more modest and this magnificent building was no more than a dream.
"Ahead were decades of spectacular national growth; an immigration program that was to change the face of Australian society and enrich the entire nation; a burgeoning of trade and cultural activity that would cement Australia's reputation as a generous and tolerant society, as a proud member of the international community and as a respected neighbour in her region.
"I believe that all this is symbolised by the Opera House itself."