from my point of view a system architect mainly has to care about
infrastructure and server components and their relationships
and connections ( Machines + Network + OS + Serversystems ).
an application architect has to care about the application
components and their relationships and their distribution
(right decomposition of an application into components + using
patterns +
building prototypes + place components along the existing infrastructure)
actually, these both skills overlap in some areas and a
cooperation between them is essentail (e.g. for sizing issues).