The 33-year-old Paris Saint-Germain centre-back hobbled off in the 27th minute of the match in La Paz.
Brazil have already wrapped up top spot in South American qualifying, having been the first nation to join hosts Russia in booking a spot at next year’s World Cup finals.
Coach Tite has called up Sao Paulo defender Rodrigo Caio, 24, to replace Silva.
“Rodrigo replaces Thiago Silva, ruled out after tests on Friday that confirmed a muscle injury to his right thigh,” Brazil said in a statement.
It is unclear how long Silva will be out of action, although his club side do not play again until a week on Saturday against Dijon, four days before a Champions League trip to Anderlecht.
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