"He is a player that won't be traveling with us but instead will work on his own," Scolari told Fox Sports news in a pitchside interview at Brazil's training ground outside Rio de Janeiro.
"Thiago is undergoing recovery work on his legs," Scolari said. "We have two friendlies and it's better to use him when he is in better or perfect condition in the second match."
Brazil face Panama in Goiania on June 3 and play Serbia in Sao Paulo three days later. The host nation open the World Cup against Croatia in Sao Paulo on June 12.
Silva, who captained Brazil to the Confederations Cup last year and is one of the first names on Scolari's team sheet, played 42 times for Paris St. Germain last season.
His place alongside David Luiz in the centre of defence will likely be filled either by Dante, the Bayern Munich defender, or Henrique, the Napoli centre half who was the surprise pick in Scolari's 23-man squad.
Doctors attended to the Shakhtar Donetsk winger but later said his injury was not serious.
The Brazilians will travel to Goiania, a city in the centre of the country, on Sunday.
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