At 1100 GMT, one million poppies were dropped over the vessel by a DeHavilland Beaver aircraft accompanied by an Auster, to mark the 90th anniversary of the end of World War I and the start of a two-minute silence.
The Duke of Edinburgh went on board to meet crew members who travelled on the vessel when it was used as a troop ship in the Falklands War in 1982.
He was introduced to former captains of HMS Ardent, Antelope and Coventry - ships that were lost in the Falklands campaign.
He then joined other guests to watch an RAF Harrier jet, from No 1 (F) Squadron, hover over the ship for about one minute at 1345 GMT, before dipping its nose in tribute.
As well-wishers looked on from packed ferries in Southampton Water, RFA Mounts Bay led a flotilla of ships past the liner, blowing its horn as it went.
In a farewell address, Cpt Ian McNaught told the crowd the vessel had been acclaimed all over the world as a symbol of British excellence.
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