You can do a
git rebase --skip
(perhaps multiple times)
That way, your applied commits will be saved. However at that point your third commit will be hidden, so follow up with:
git branch old-commit ORIG_HEAD
to have access to your other (third an following) commits.
For finishing touch, you could do
git checkout old-commit && git rebase --interactive HEAD...master
and remove the successfully rebased commits.