Put your server into maintenance mode using this plugin.
All online players will be kicked on initialising of the maintenance mode with the exception of players with bypass or OP permission.
Players without bypass permission or OP will be unable to join the server while maintenance is active.
You may set the message to be displayed during maintenance in the config.yml.
/maintenance
Tells the executing player if the server is in maintenance mode or not.
Permissions: spigotmaintenance.info
/maintenance enable
Enable maintenance mode.
Permissions: spigotmaintenance.enable
/maintenance disable
Disable maintenance mode.
Permissions: spigotmaintenance.disable
spigotmaintenance.bypass
Players with this permission are allowed to join the server during maintenance.

