A control system for an engine includes first and second modules. The first module estimates a total amount of exhaust gas recirculation (EGR) in the engine, wherein the total amount of EGR includes (i) EGR within cylinders of the engine and (ii) EGR flowing through an EGR system of the engine. The second module selectively controls an overlap of intake and exhaust valve timing in the engine based on (i) a position of an EGR valve in the EGR system and (ii) a comparison of the estimated total amount of EGR in the engine and an EGR threshold.