The 25 year old was replaced at half-time in the Uefa Nations League clash as the Netherlands claimed a point in what was an epic 2-2 draw.
De Ligt set up Germany’s Deniz Undav for an equalising goal before his failed clearance led to Joshua Kimmich giving Germany the lead before half time.
Koeman spoke about the decision to take him out the game.
“Of course I would rather have kept (Matthijs de Ligt) on the pitch," Koeman told Dutch broadcaster NOS.
“It just looks like he is now in a period where all his mistakes are being punished.
"I gave him a new chance today but eventually I protected him by taking him off."
In his press conference on Monday before the draw against Germany, he spoke on the defender and how he was unable to mark 38-year-old striker Edin Dzeko in their win over Bosnia and Herzegovina.
"He did not get his footwork right. It was a bad individual moment for a defender. You have to learn from that, it is clear that these kinds of moments need to be improved.
"But we should not be dramatic about it and put too much emphasis on it."