HMS Prince of Wales limped back to Portsmouth Naval Base on Saturday after a coupling on its starboard propeller shaft broke.
The £3 billion aircraft carrier will now need to go into dry dock, probably at Rosyth in Scotland, to undergo repairs.
Families of crew members and well-wishers lined the walls of Portsmouth Harbour and waved Union flags to see HMS Queen Elizabeth off.
The crew were notified last week that they would be sailing to the US, altering previous plans for deployments to the Baltic and Mediterranean this autumn.
The Navy has not detailed which of HMS Prince of Wales’s diplomatic engagements and military exercises will be carried out by HMS Queen Elizabeth.
The programme included flight trials with F-35B Lightning jets, the Atlantic Future Forum and port stops in New York, Halifax in Canada, and the Caribbean.
Shortly after the Prince of Wales, the Nato flagship, set sail on Saturday August 27, a mechanical fault was discovered with the starboard shaft.
The departure of the 65,000-tonne ship had already been delayed from the previous day because of a technical problem but a decision was taken to sail anyway.
The carrier returned to Stokes Bay in Gosport, Hampshire, two days later, travelling at a rate of four knots and accompanied by tugs for the journey to calmer waters.
Navy divers have been inspecting the ship and found that a coupling on the starboard propeller shaft had failed.
Rear Admiral Steve Moorhouse, director of Force Generation, who is responsible for making sure Royal Navy ships are ready to deploy, confirmed on Friday that HMS Queen Elizabeth would take over the US duties.
He said: “Royal Navy divers have inspected the starboard shaft of the ship and the adjacent areas and they have confirmed there is significant damage to the shaft on the propeller and some superficial damage to the rudder but no damage to the rest of the ship.
“Our initial assessment has shown that coupling that joins the final two sections of the shaft has failed.
“Now, this is an extremely unusual fault and we continue to pursue all repair options.”