The new £4.3 billion terminal was opened by the monarch amid strict security.
The Queen was greeted by 800 specially invited guests, including business and airport workers at Heathrow, where she described the new terminal as "a highly impressive, 21st century gateway to Britain and the wider world".
The Queen also met with the crew of the Boeing 777, which crash-landed at the airport in January.
The Queen opened Heathrow's first passenger terminal, the Europa Building - now called Terminal 2 - back in 1955.
The Terminal 5 project team has successfully erected the UK's biggest free-standing building; moved the 900-tonne top cab of a new 87m high control tower 2km across the airfield; tunnelled over 13km for rail and baggage links; diverted two rivers; and installed over 30,000 sq metres of glass building facades. All Terminal 5's footprint is contained within a former sludge works at the western end of the existing airport, situated between the two runways, adjacent to the M25.
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The Terminal 5 complex features 60 new aircraft stands; two satellite buildings, the second phase of which will be completed by 2010; rail links to London Underground and Heathrow Express; a new multi-storey car park; and extensive landscaping.
The building was designed by 2006 Stirling Prize winner Rogers Stirk Harbour and Partners.
Sir Nigel added: "From every perspective, this is a landmark project and I am proud to think that Terminal 5 has become a model construction project, setting new, higher standards for an industry around the world."
Sir Nigel Rudd, chairman of BAA, said: "Terminal 5 marks the start of a new beginning for Heathrow, for BAA and for our millions of passengers. It is, by any standard, a triumph of ambition, commitment and collaboration. It will breathe new life into Heathrow, allowing us to continue our transformation of the rest of the airport and will put Heathrow and BAA back where they belong - at the leading edge of global travel."
Willie Walsh, British Airways Chief Executive, said: "Terminal 5 is a fantastic facility and our customers will really enjoy the space, comfort and convenience it offers. The customer experience at Terminal 5 will rival, if not exceed, that at any airport in the world."
Around 60,000 people have worked to build Terminal 5, since construction work began in September 2002.
The opening of the terminal comes just 24 hours after a man was arrested after running onto the north runway at Heathrow with a rucksack. He was arrested by armed officers and a controlled explosion was carried out on his bag. No explosives were found. He remains in police custody.
The new terminal, which will be occupied by British Airways exclusively, will become operational on March 27.
The terminal, which will be able to handle 30 million passengers a year, features the largest airline lounge complex in the world.
Airport operator BAA said that the new terminal would transform the level of passenger service at Heathrow and help to ease queues at check-in desks and security checks.
However, environmental and residents' groups are opposed to the new terminal, arguing that it will eventually mean an increase in flights, noise and pollution.
(KMcA/JM)
