A control system for an engine includes a first spark control module and a second spark control module. The first spark control module retards spark timing for M of N cylinders of the engine to a first spark timing during a period before deactivating or after reactivating the M cylinders, wherein M is an integer greater than or equal to one, and wherein N is an integer greater than M. The second spark control module advances spark timing for (N−M) active cylinders of the engine to a second desired spark timing during the period before deactivating or after reactivating the M cylinders, wherein the second spark timing is greater than the first spark timing.