An apparatus in one embodiment includes at least one processing device configured to receive at least one notification from a switch of a switch fabric coupled between one or more host devices and a storage system, to select a particular one of a plurality of zoning sets based at least in part on the one or more received notifications, and to send an indication of the selected zoning set to the switch. The indication of the selected zoning set illustratively comprises a command that instructs the switch to alter its zoning configuration in accordance with the selected zoning set. In some embodiments, the processing device comprises a data protection appliance coupled to a storage area network that includes the switch fabric. The switch may comprise a Fibre Channel (FC) switch of an FC switch fabric, and the notification may comprise a fabric performance impact notification (FPIN) generated by the switch.