This document discusses gauge invariance of the action principle for gauge systems with noncanonical symplectic structures. It shows that for such systems, the complete set of commuting observables at the time boundary is now fixed by the boundary term and the symplectic structure, rather than just the canonical symplectic structure. The theory is applied to two nontrivial models with SL(2,R) and SU(2) gauge symmetries whose phase spaces have new interactions due to noncanonical symplectic structures.