Launch Beyond Compare, go to the Beyond Compare menu and run Install Command Line Tools.
Diff
$ git config --global diff.tool bc3
To launch a diff using Beyond Compare, use the command:
$ git difftool file.ext
Merge (Pro only)
$ git config --global merge.tool bc3
$ git config --global mergetool.bc3 trustExitCode true
To launch a 3-way merge using Beyond Compare, use the command:
$ git mergetool file.ext