Controlling a Battlefield 3 server is best suited to Procon. You can obtain the software from http://phogue.net.

After launching Procon, click "Create Connection" on the right of the program's start page.

You should complete the fields that now appear as follows:

Hostname/IP: IP of the game server without the port

Port: 47200

Username: Leave this field blank

Password: The server's Rcon password

Then click "Connect".