See for example binutils and ld (2.27)
https://www.gnu.org/software/binutils/
Or rust (which is at version 1.11) or idris (0.12)
Using groups of numerals separated by decimal points to communicate this not-decimal nature is, however, a potentially very confusing overloading of notation (and, actually, while most version numbers using notation that looks like that now don't have decimal number semantics, that's not historically universally true; version numbers that were -- at least to the extent of comparing as -- decimals were actually quite common in the past.)
If you want to use a decimal-imitative notation, do like Knuth and have your system's version number converge to Pi or e or some other constant.
Wikipedia [1] says it was common in the 1980s, but gives two only two modern examples: Opera and Movable Type. And even that seems to be outdated. Neither of them uses decimal version numbers any more. Can you think of any others?
I had long preferred either Real/decimal numbers as version numbers or hierarchy-of-decimal-digits (exactly one digit each, e.g. "1.9.9" must progress to something like "1.9.9.1" or "2.0.0"). But semantic versioning is really popular these days, so I'm much less surprised even if it's not my preference.