From Using Beyond Compare with Version Control Systems - Git for Windows:
Note: If you use the Git for Windows' Bash Command Prompt instead of the default Windows Command Prompt, you need to escape the $ character with .
For Git 1.7.6 and newer, edit the global config file to set the path
Diff
At a Windows command prompt enter the commands:
git config --global diff.tool bc3 git config --global difftool.bc3.path "c:/program files/beyond compare 3/bcomp.exe"
To launch a diff with BC3, use the command "git difftool foofile.txt".
3-way Merge (v3 Pro)
At a Windows command prompt, enter the commands:
git config --global merge.tool bc3 git config --global mergetool.bc3.path "c:/program files/beyond compare 3/bcomp.exe"
Use
git merge
for the regular merge andgit mergetool
for the Beyond Compared based merge.
This worked fine with BCompare-3.3.8.16340.exe and Git-1.8.4-preview20130916.exe:
C:\su-q>git difftool "HEAD^" Viewing: 'README' Launch 'bc3' [Y/n]: Viewing: 'bag_frame.gif' Launch 'bc3' [Y/n]: