The Spanish giants crushed Qatar's Al Sadd 4-0 in Yokohama, hardly breaking sweat, but the victory was marred by the injury to Villa, who snapped his left shin in the first half.
"The players all felt sick for David after the game," Barcelona coach Pep Guardiola told reporters. "They are very down. I told them it can happen to anyone at any time.
"David is going to be out for a long time and now we will have to win the Club World Cup without him. It will take a long time to return from this kind of break."
Barca, bidding to win the seven-team tournament for the second time in three years, take on Brazil's Santos and their talented teenage striker Neymar in Sunday's final.
The Catalans closed training to the media on Friday following the injury blow to Villa, who is expected to be out for up to five months.
"This will be an extremely difficult time for David," Barcelona captain Carles Puyol said, echoing the sentiments of his coach.
Villa's injury is also a setback for World Cup holders Spain as they prepare to defend their European Championships title in Poland and Ukraine next year.
"Our thoughts are with our player who must return for an operation," Guardiola snapped when asked who would replace Villa in the final. "Don't ask me about tactics now."
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Puyol grimaced when asked about stopping Neymar, who has turned down a fortune from several top clubs in Europe to stay at Santos until after the 2014 World Cup in Brazil.
"It will be very difficult to mark Neymar," Puyol said of the 19-year-old. "He's got such great speed. He's already a great player and has fantastic potential for the future.
"He has quick feet and does amazing things. He can switch from right to left or left to right so he's very unpredictable when he gets on the ball.
"Everyone is talking about Neymar but Santos have many dangerous players."
Argentine midfielder Javier Mascherano, who also picked up a knock against Al Sadd, promised Barca would not underestimate the South American Libertadores Cup holders.
"Santos are a very good side and they have some quality players in attack, like Neymar and [Paulo Henrique] Ganso," said the former Liverpool enforcer.
"They have experience and their coach [Muricy Ramalho] is very clever. We have a lot of respect for them. Right now though we all feel terrible for David and need to support him."
