Yes. The usual ports that you mention are the conventional analogue ones, with separate channels for L/R information. S/PDIF ports are digital, and come in two flavours, namely coaxial and optical. In both cases, the L/R channels (and other data) are multiplexed together for transmission over this medium. It is the job of the amplifier or other device that the other end of the lead is plugged into to recover and separate the signals and data appropriately.
See: S/PDIF - Wikipedia, the free encyclopedia