The 27-year-old prince addressed coach Fabio Capello and the players on Friday, shortly after Ferdinand hurt his left knee in training and was ruled out of the tournament.
"Despite Rio Ferdinand's injury, which is a disappointment for Rio himself and the England team, morale in the team is high," William said in a statement. "The whole country is behind them."
Football Association general secretary Alex Horne said that William, who is second in line to the British throne, provided "a real morale boost for everyone at the FA ahead of the World Cup, and the England players and management really appreciated the message of support."
William will be traveling to Cape Town to watch the team's second match against Algeria on June 18. The United States and Slovenia are also in Group C, with England opening against the Americans on June 12.
William, president of the Football Association, spoke to the England camp from Wembley Stadium after meeting members of the 2018 World Cup bid team.
"All the staff at Wembley and the players and management in South Africa are working so hard to make this a successful year for English football," said William, who supports Aston Villa. "It could be a year of amazing achievement, on and off the field — we could win both the World Cup in South Africa and the World Cup vote in Zurich. It will certainly be tough, but both are doable."