The structures of my Git repositories look like this:
A-B-C-D-E-F # master branch in separate repo1
A-B-C-D-E-G-H # master branch in separate repo2
Your picture suggests that you don't really want to "combine the two repositories" so much as merge commits G and H in to repo1. You should be able to do something as simple as add repo2 as a remote to repo1 and fetch/pull the changes in.
You can treat another git repository on the same filesystem as a remote repo.
In the first, do the following:
git remote add <name> /path/to/other/repo/.git
git fetch <name>
git branch <name> <name>/master #optional
Now they're both branches in a single repository. You can switch between them with git checkout, merge with git merge, etc.
I think Jim is right. Also bear in mind that if two commits do exactly the same patch/diff against the code, they will have exactly the same SHA1 hash. So A through E should have the same SHA1 in both repos, so it shouldn't be a problem to merge from one to the other, and keep the merged repo as the sole repo to move forward with.
You can setup on repo1 a tracking branch for repo2, and then keep them distinct that way, and delay the merge to whenever you want.