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Your perfect vacuum is not perfect. There is a bit of mercury vapor for example that will always be there. Again, a perfect vacuum is not possible on macroscopic scales.
To say that the vacuum has no temperature depends on your definition of temperature. The usual one that people throw around is kinetic energy of molecules. This is however not precise. E=n/2kT for n degrees of freedom, but this depends on "degrees of freedom" meaning a very specific thing which doesn't always hold. In any case, that formula (and its inadequacies) come from a deeper definition. Its fairly involved, so I won't get into it. The basic idea, though, is that objects are said to be at the same temperature if they can be brought into contact with one another without heat (non-mechanical energy) flowing between them. So matt_mll's radiation would actually be said to be at a certain temperature even without matter being present. Its just semantics though.
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