The Croat says neither player will be punished following their clash on Thursday while preparing for Sunday's Bundesliga match at Fortuna Dusseldorf.
"The three of us talked about it. The players are sorry and have apologised for their behaviour," said Kovac.
"There will be no financial penalties and the matter has been resolved."
The German champions went top of the league by one point last weekend by beating previous leaders Borussia Dortmund 5-0.