Santos was sent away from the touchlines by Australian match referee Ben Williams prior to the penalty shut-out that saw his side dominated 5-3 by Costa Rica, who went on to a quarter-final meeting with the Netherlands.
Santos got into an exchange with the official and was forced to watch the penalty shoot-out from an office in the belly of the Arena Pernambuco.
"There was television set in the back, that's where I saw the penalty shoot-out," said Portuguese coach Santos, who hit out at the referee's decision.
"The referee tried to stop me and when I protested by saying the entire Costa Rican squad is on the pitch, why can't I go on, he said you can't talk like that to me, and ordered me off."
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As well as seeing his side fail to extend their history-making run at the tournament -- Greece were appearing in the last 16 for the first time --- Santos also found out the Greek federation held little belief of their quarter-final chances.
Santos, whose contract runs out on Monday, added: "Greece already has a new coach. That's been announced.
Talking about the moment Costa Rica goalkeeper Keylor Navas stopped Theofanis Gekas's spot-kick during the decisive penalty shoot-out, he added: "Definitely sadness. Not much else goes through your mind at that time.
"We reached a landmark for Greece. We wanted to go on to the quarter-finals in Salvador, that's why we're sad.