Several people have mentioned the need to restart the servlet container if Jenkins is not running as a standalone. But Tomcat (or what is being used) doesn't need to be restarted. Tomcat can force a restart of the Jenkins context if your Jenkins restart is hung.
But to address another comment, when you put Jenkins in the "shutting down" mode it will not actually shut down. It stops new jobs from executing and place a giant red banner on the system pages so everyone knows that the administrator wants to take it down eventually. There are plugins to trigger a servlet container restart for that context after all builds are completed.
The alternative is to wait till the last running job completes, then manually kick over Jenkins from the container (or via the command line options that others have mentioned for the standalone Jenkins install).