git-remote-gcrypt is a git remote helper to push and pull from repositories encrypted with GnuPG, using a custom format
Supported backends are local, rsync:// and sftp://, where the repository is stored as a set of files, or instead any where gcrypt will store the same representation in a git repository
The aim is to provide confidential, authenticated git storage and collaboration using typical untrusted file hosts or services.

Tested: it works fine and is very easy to setup:

git remote add gitcrypt gcrypt::git@...
git config user.signingkey ...
git config gcrypt.participants ...
git push gitcrypt master

To encrypt only SOME files in a git repo, better look at git-crypt