De Ligt, 25, was replaced at half-time in the Uefa Nations League clash in Amsterdam by Brighton’s Jan Paul van Hecke after the defender had a hand in both of Germany’s first-half goals.
A misplaced pass in the first half led to Deniz Undav equalising before his failed clearance led to Joshua Kimmich giving Germany the lead, just three days after De Ligt made mistakes in the Dutch’s 5-2 win over Bosnia and Herzegovina.
“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.”
Koeman spoke publicly on De Ligt’s performance in their win on Saturday, where he was unable to mark 38-year-old striker Edin Dzeko as he scored Bosnia’s second goal in Amsterdam.
“We have discussed it,” Koeman said in his press conference on Monday before the draw against Germany.
“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.”
De Ligt, who has 45 international caps, only joined United last month from Bayern Munich in a deal worth over £42m (including add-ons).
Competing with De Ligt in Koeman’s squad for minutes are fellow Premier League defenders Virgil van Dijk, Nathan Ake, Micky van der Ven, Jurrien Timber, Van Hecke and Sven Botman, who is currently injured.
During the 2-2 draw, Manchester City’s Ake was stretchered off in the first half with what appeared to be a hamstring injury.