Bitcoind is either a) the RPC server or b) an RPC client.
Bitcoin-Qt is a GUI + optionally the RPC server.
The error you're getting probably means you're already running bitcoind as RPC server, so you can't start Bitcoin-Qt in server mode as well.
Shut bitcoind down (./bitcoind stop), start Bitcoin-Qt with -server, and after that point you can send RPC commands to the GUI.
Aaah, now I get it!
So I was in fact running bitcoind and then trying to start bitcoin-qt as a server, which can't work.
So, my new question, now, is: Can I connect bitcoin-qt as a "client" to a constantly running bitcoind?
As I understand, that's what OP was actually asking. He probably changed his plans with "-server".
Now I think this isn't possible at all.. Then I would write a script to stop bitcoind and start bitcoin-qt automatically, when needed.