The Portuguese coach was forced to hold peace talks with defender Giannis Maniatis after he reportedly prepared to fly home following an argument with Georgios Tzavellas
Olympiacos' Maniatis lashed out at fellow defender Tzavellas over the quality of crosses the PAOK man was delivering at training, and the former reportedly booked a flight home to Greece after storming off the training pitch.
There was a heated exchange between the pair, with unrest emerging in the camp after Greece suffered a dismal 3-0 loss to Colombia to open their World Cup campaign in Brazil.
Santos was forced to counsel Maniatis and convince him to remain with the squad ahead of their crucial tie with Japan in Natal on Thursday, but the Portuguese boss insisted the bust-up was over.
''I am convinced (it is over) because I had a conversation with both players," Santos said.
"Me and my staff talked to both of them before I took my decision for tomorrow's first XI.
"It was a long and personal conversation, it was not by phone. For me it became absolutely clear that everything was over."
Santos stressed he was eager to recover from their disappointing opening loss as they seek a vital three points against Alberto Zaccheroni's side.
"That is football. Sometimes football brings bad things," Santos said.
"But now we have to think positively. We have to forget what happened and look forward to making history.
"That means going forward in the World Cup.
"And for that, we have only one option, which is facing this match against Japan seriously as we always do and try to win it."