France came from behind at home thanks to a brace from Antoine Griezmann, after Toni Kroos had put Germany ahead early on with a spot-kick of his own.
Griezmann's clincher from 12 yards came with 10 minutes remaining, when Mats Hummels' foot was trodden on by Matuidi as he attempted to make a sliding challenge, and referee Milorad Mazic pointed to the spot on Tuesday.
Low has no doubt France were lucky to get the decision, though he was generally content with his team's performance, adamant they were no worse than the world champions.
"It was not a penalty," Low told ARD after the match. "Mats does not touch him. Matuidi steps on his foot.
"We were absolutely on par with the world champions, but we had to score a second goal in the first half.
"Unfortunately, we were not rewarded for a good game. If we were a bit smarter then we would've scored the second goal and won."
Germany went into the match on the back of a 3-0 defeat to Netherlands in the Nations League on Saturday and Low made five changes to his starting XI.
Despite the alterations, he was quick to insist his older players are not finished yet.
"The French did not cope with our setup in the first half," he added. "France had little access and we always found solutions.
"After the game against Netherlands, it was clear that we had to change something. If you want to be permanently successful, you need a good mix of older and younger players. The old players have not forgotten how to play football."