Yes you can if you use Samba to share the target drive. (Or install netatalk for your linux server to actually serve up an Apple share.) The file system itself doesn't really matter. How you share the drive over the network is what's important. (The linux OS will handle reading and writing to the ext3 filesystem via Samba, or NFS, or AFP.)
You'll also have to force Time Machine to see network shares as well. (It doesn't do it by default.)