The eight-metre high waves left 14 people injured, including one woman who remains in a "very serious condition" in hospital.
"It was a monster wave... it smashed all the windows. Everything happened so quickly," German passenger Margrit Woffe-Ternes told Spanish television.
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Images filmed by one passenger showed screaming people fleeing as a wall of water crashed through a window and then swept into a lounge area, knocking over furniture.
"It was a tragic moment, water was coming in from all sides and the boat shook," Italian passenger Ervico Curtis told the website of daily newspaper El Pais.
"We didn't know what was happening, if there were dead or injured, only that we were going back to Barcelona," another Italian passenger identified as Franco told Spanish television.
One German and one Italian passenger were killed in the accident on Wednesday evening as the ship was off the coast of Spain, the owners, Cyprus-based Louis Cruise Line, said.
Windows smashed
One 64-year-old woman, was in "very serious" condition, a spokeswoman at Barcelona's Vall d'Hebron Hospital said. Spanish media said the woman's legs were broken in the accident.
A 59-year-old man was also hospitalised with multiple injuries.
Most of the 1,300 tourists on board the ship at the time of the accident were repatriated from the Mv Louis Majesty to their home countries on Thursday.
The 200-metre ship was on a 12-day cruise of the western Mediterranean with 1,350 passengers and 580 crew when it was hit.
It docked in Barcelona late Wednesday to evacuate the dead and injured and carry out repairs.
"I wasn't scared but I am very happy to be going home now," German passenger Brigitte Himmelhan, who was in the ship's theatre when the waves hit, told El Pais.
The company said in a statement that the passengers were killed when the freak waves smashed windows in a public area at the front of the ship.
Unpredictable phenomenon
Louis Cruise spokesman Michalis Maratheftis said there would be no investigation.
"This was a natural, unforeseen and unpredictable phenomenon because we are talking about three big waves, higher than eight metres, striking the vessel," he said.
"This is not an incident which we could have prevented, therefore there will be no investigation.
"All passengers are on their way back to their respective countries as we speak. We have made all the necessary arrangements for all of the passengers to be safely transported back to their countries," Maratheftis said.
But an expert from the French national weather agency, Jean-Michel Lefevre, said the cruise ship was in heavy seas where eight-metre waves were to be expected.
"The conditions were favourable to the formation of waves higher than normal," he said.
Ship undergoing repairs
The Maltese-flagged ship was to remain in Barcelona for repairs before sailing back to the Italian port of Genoa where normal operations would resume on March 12.
Experts say rogue waves are almost always generated by storm-related winds.
"They always come when you are least expecting it," said Michel Olagnon, a specialist on the phenomenon at the French Sea Institute (Ifremer) in Paris.
Once possible scenario for Wednesday's monster waves could be a phenomenon of amplification whereby two or more waves overlap.
"As wind increases in intensity, it is first going to create relatively small waves, and then bigger ones, which travel faster," said Christain Kharif, a French oceanographer and co-author of "Rogue Waves in the Ocean".
"Eventually the big ones will catch up, and the energy is concentrated as the waves pile up," he explained.
