Britain's monarch stepped out with the Duke of Edinburgh at Rosyth Dockyard to christen the 65,000 tonne vessel, which is 280m long by 70m wide.
Instead of smashing a bottle of champagne on the boat, as is traditional in ceremonial ship launching, the Queen fittingly launched the Scotland-built warship with a bottle of Islay single malt whisky.
The bottle was also released, not by cutting a ribbon, but when the monarch pressed a large green button from a platform offering a good view of the impressive ship.
Addressing the audience, which included Prime Minister David Cameron, Chancellor of the Exchequer George Osbourne and Scotland's First Minister Alex Salmond, the Queen said the "innovative and first class" warship marked an "exciting new era" for the Royal Navy.
"In sponsoring this new aircraft carrier, I believe the Queen Elizabeth will be a source of inspiration and pride for us all," she said. "May God bless her and all who sail in her."
Programme director Ian Booth of the Aircraft Carrier Alliance, which oversaw the ship's construction, told the audience HMS Queen Elizabeth "breaks new ground" in naval technology.
"The ship truly reflects the very best of British design and ingenuity," he said. "We all feel an enormous honour to see Her Majesty name her today."
Friday's engagement was a special moment for the Queen as she has not named a ship for more than 15 years.
HMS Queen Elizabeth, which is taller than Nelson's Column, has been worked on by over 10,000 workers at a projected cost of £6.2bn.