Robert Salmond, who served in the Royal Navy during the Second World War as a petty officer on two aircraft carriers, joined his son along with Prime Minister David Cameron and other leading politicians at the ceremony for HMS Queen Elizabeth.
The veteran Scot, who repaired the radios on planes, was on the fleet carrier HMS Indomitable when she was torpedoed while supporting the invasion of Sicily in 1943. Prince Philip commanded the destroyer HMS Wallace in the same action.
Later, the First Minister's father saw action in the Salerno landings in Italy before he was diagnosed with tuberculosis. He remained in hospital for the rest of the war.
In 2011, on his 90th birthday, the veteran officer climbed the gantry to the controls of the main crane as work began on the £3.1 billion vessel.
"My father never spoke too much about the war when I was growing up. However, we are all proud of him, as are all families of those who served," said Mr Salmond.
He said the damage to the Indomitable almost certainly saved his father's life because when the navy detected TB on board it screened the previous crew, including Mr Salmond Senior, who tested positive.
"So if it hadn't been for a Junker's bomber putting a hole in his ship, father would have been dead and I wouldn't have been born," explained Mr Salmond. He added: "He will love seeing the launch of the new carrier."
The Queen, who was accompanied by the Duke of Edinburgh, oversaw the traditional naming ceremony by pressing a button to release a bottle of Islay malt whisky - suspended at the front of the ship - to smash on to the hull.
About 3,500 people involved in the design and construction of the carrier watched the celebrations, alongside dignitaries and politicians including First Sea Lord Admiral Sir George Zambellas, Labour leader Ed Miliband and Defence Secretary Philip Hammond.
Also attending the ceremony were Chancellor George Osborne, Chief Secretary to the Treasury Danny Alexander and Scottish Secretary Alistair Carmichael, as well as former prime minister and Kirkcaldy and Cowdenbeath MP Gordon Brown.
The RAF's Red Arrows performed a fly-past during the event, painting the sky over the Forth red, white and blue.
The fly-past was followed by a procession of three generations of Royal Navy aircraft, including a historic 1950s de Havilland Sea Vixen fighter - the last and only flying aircraft of its kind in the world.
Aircraft Carrier Alliance managing director Ian Booth, the man overseeing the construction of the ship, said: "This is a historic occasion for our country and a proud moment for more than 10,000 people across the UK who have worked together to deliver HMS Queen Elizabeth.
"This is an engineering challenge of unprecedented scale and complexity for UK shipbuilding and I want to congratulate everyone involved in making today possible.
"The ship truly reflects the very best of British design and ingenuity and we all feel an enormous honour to see Her Majesty name her today."
The naming ceremony, a naval tradition dating back thousands of years, marked the first time in more than 15 years that the Queen has christened a Royal Navy warship.
It comes five years after the first metal was cut on the vessel and 33 months after the first section entered the dry dock at Rosyth for construction to begin.
The ship and a second vessel, the under-construction HMS Prince of Wales, are the largest warships ever built for the Royal Navy.