The two-level systems (TLSs) naturally occurring in Josephson junctions constitute a major obstacle for the operation of superconducting phase qubits. Since these TLSs can possess remarkably long decoherence times, we show that such TLSs can themselves be used as qubits, allowing for a well controlled initialization, universal sets of quantum gates, and readout. Thus, a single current-biased Josephson junction can be considered as a multiqubit register. It can be coupled to other junctions to allow the application of quantum gates to an arbitrary pair of qubits in the system. Our results indicate an alternative way to realize superconducting quantum information processing.