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, and the unrest comes after Greece suffered a horrendous 3-0 loss to Colombia to open their FIFA 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.
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 said he was looking to advance past their poor loss to the Colombians, with games against the Japanese and Ivory Coast their chances to turn their form around.
"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."
