If you add the --preserve-merges option (or its synonym, -p) to the git rebase -i command then git will try to preserve the merges when rebasing, rather than linearizing the history, and you should be able to amend the merge commits as well:
git rebase -i -p HEAD~5
Note. --perserve-merges has been deprecated in favour of --rebase-merges as of git v2.22 (https://www.infoq.com/news/2019/07/git-2-22-rebase-merges/).