Kovac admitted the forwards traded blows following an argument at a training session behind closed doors on Thursday while preparing for Sunday's league game away to Fortuna Duesseldorf.
"The three of us talked about it, the players are sorry and have apologised for their behaviour, there will be no financial penalties and the matter has been resolved," said Kovac in a press conference.
Lewandowski, 30, reportedly chastised Coman, 22, during a training exercise, and the exchange of words quickly escalated.
The two players were reportedly separated by defenders Niklas Suele and Jerome Boateng, but Kovac was evasive about the cause of the strife, saying simply "emotions" had run high in a heated training session.
Bayern are a point clear at the top of the Bundesliga after their 5-0 demolition of title rivals Borussia Dortmund last week.
Yet Kovac's side are still feeling the pressure with six games to go, especially as club chairman Karl-Heinz Rummenigge has said Bayern's head coach does not have a job guarantee.
"I will concentrate only on football and won't add my thoughts to every little thing - my job as coach has become a side issue and I want to concentrate on the core business at hand," said Kovac.
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