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There has been speculation Miranda, who has been in outstanding form for Atletico Madrid, would receive his first international call-up in over a year, but Scolari opted to name Napoli's Henrique as his fourth centre-back.
"He's a player I have a lot of trust in," Scolari said of Henrique.
The latter's Anfield team-mate Coutinho has been in superb for this season, but Scolari elected to include just two attacking midfielders in Chelsea pair Oscar and Willian.
The 65-year-old called Rafinha and Fernandinho up for the first time for Brazil's most recent friendly – the 5-0 win in South Africa in March – but while the Manchester City midfielder retained his place, Inter veteran Maicon was preferred to the Bayern Munich man.
"If I'd had the choice, I would have played in World Cup qualifying," he said.
"It's important practice. We had the Confederations Cup, which was a good experience, but it was only a few games."
Scolari's men open the tournament against Croatia in Sao Paulo on June 12.
