git-subtree is a script designed for exactly this use case of merging multiple repositories into one while preserving history (and/or splitting history of subtrees, though that is seems to be irrelevant to this question). It is distributed as part of the git tree since release 1.7.11.
To merge a repository <repo> at revision <rev> as subdirectory <prefix>, use git subtree add as follows:
git subtree add -P <prefix> <repo> <rev>
git-subtree implements the subtree merge strategy in a more user friendly manner.
The downside is that in the merged history the files are unprefixed (not in a subdirectory). Say you merge repository a into b. As a result git log a/f1 will show you all the changes (if any) except those in the merged history. You can do:
git log --follow -- f1
but that won’t show the changes other then in the merged history.
In other words, if you don’t change a‘s files in repository b, then you need to specify --follow and an unprefixed path. If you change them in both repositories, then you have 2 commands, none of which shows all the changes.
More on it here.