The experienced Real Salt Lake striker - who has scored 32 goals in 93 appearances for his country - suffered a foot injury during training on Thursday and will miss the showpiece in Brazil as a result.
It represents a huge blow for Jorge Luis Pinto, who must now come up with an alternative plan to get his side out of Group D - a pool that includes England, Italy and Uruguay.
Pinto's penultimate chance to test out alternative tactics ahead of their opener against Uruguay will come on Monday when they face Alberto Zaccheroni's side in Tampa.
Costa Rica are also without the versatile left-sided Bryan Oviedo due to a broken leg but Pinto is confident his team can still produce the goods without two of their more established players.
"After analysing the doctors' opinion and talking with the player, we have to face the reality," Pinto told a press conference.
"Alvaro will not play at the World Cup. We hope he recovers on time to travel with us to Brazil. It really hurts, because he's an extraordinary man.
"It will be tough to replace him. We are ready for a situation like this."
Following qualification for the World Cup, Costa Rica were beaten by Australia, Chile and South Korea without scoring a goal.
However, they returned to winning ways against Paraguay in March with Saborio and Joel Campbell on the score sheet.
And Pinto will hope any changes in personnel or tactics will come to fruition against a Japan side who looked out of sorts against Cyprus on Monday.
Atsuto Uchida's goal before the break gave them a third consecutive victory but they were far from convincing against a side ranked 130th in the world.
They showed little of the attacking intent that was on show in their wins over Belgium and New Zealand - but Zaccheroni is not worried by their showing against the Cypriots.
He feels both fitness and performance levels will grow as they edge closer to their World Cup opener against the Ivory Coast in Group C.
"I am very satisfied with the way it went," he said after the win in Saitama.
"We had three players back from injury and I'm satisfied with the way they played. We still have two games left and I want to give them all more time as the games come.
"I especially want to improve the speed of play. Physical condition equals speed."
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