You could use opendiff. It is a command line tool which opens the GUI of FileMerge.
You could instruct Git to use it automatically for git-mergetool with:
git config --global merge.tool opendiff
If you want it for git-difftool as well:
git config --global diff.tool opendiff
And you could also disable the prompting for every file with:
git config --global difftool.prompt false
For more details type: git help config and search with / for the different options.
P.S. If you don't have opendiff installed you could install it together with the Developer Tools from Xcode: https://developer.apple.com/library/mac/documentation/Darwin/Reference/ManPages/man1/opendiff.1.html
UPDATE: In recent versions of Xcode, FileMerge is now bundled with Xcode. You cannot install FileMerge as a standalone program. opendiff is still in its command-line utilities which are standalone.