Serge Gnabry's superb finish on the hour secured a point in Nations League Group A4 for Germany, who had to come from two goals down in Cologne.
Switzerland raced into a 2-0 lead through Mario Gavranovic and Remo Freuler, though Timo Werner swiftly pulled one back before Kai Havertz equalised.
Gavranovic's second put Switzerland back ahead, only for Gnabry to restore parity once more with his 14th international goal since November 2016.
Though Kroos made a landmark appearance, his error ultimately led to Switzerland's second goal, and though content with reaching a century of caps, the 30-year-old said winning titles means much more to him than personal accolades.
"It was of course a special game for me. To have reached 100, that's a nice mark. But anyone who knows me knows that I care more about results and titles than appearances," Kroos said.
"But of course, 100 games is something nice. In the past I have played with incredibly good footballers and guys. I hope that we can build on these successes with the current team.
"Our problem was the first 10 or 15 minutes. After that we played a good game and improved our footballing skills to the last game. In the end we are not satisfied with the point because we aim to win the game."
Kroos is one of the old guard in Germany's squad, with Joachim Low having stood by his decision not to select Mats Hummels and Thomas Muller, despite the latter's sensational form for Bayern Munich.
Havertz, who took his goal brilliantly and looked sharp alongside his Chelsea team-mate Werner, believes the comeback is a step in the right direction for Germany, who have managed just one win so far in 2020.
"We came back after many setbacks, we showed our morals," Havertz said. "We are in a process, we have a young team. We will not be dissuaded from our path and will keep trying. We have to defend more intelligently, but we saw good beginnings today."
Head coach Low added: "The game was incredibly intense. Both teams risked a lot, but also made a lot of mistakes.
"We got into the game badly, then we showed very good morale. That was certainly positive. But we made some mistakes at the back. We consciously risked a lot, made mistakes, we have to fix that."