The Git program can store both, and you can explain to it that differences in the Markdown file correspond to the differences in the document file. Pandoc is a tool worth knowing about anyway.

The git program is incredibly self-aware, so its auto-complete options effectively provide an alternative interface. You can start by exploring all of git’s subcommands by typing git followed by ...

When you type git, that's just telling the command line that you want to use the git program. When you type commit, you're telling git you want to use the commit command.