A simple but working way is first to list all installed plugins, look for updates and install them.
java -jar /root/jenkins-cli.jar -s http://127.0.0.1:8080/ list-plugins
Each plugin which has an update available, has the new version in brackets at the end. So you can grep for those:
java -jar /root/jenkins-cli.jar -s http://127.0.0.1:8080/ list-plugins | grep -e ')$' | awk '{ print $1 }'
If you call install-plugin with the plugin name, it is automatically upgraded to the latest version.
Finally you have to restart jenkins.
Putting it all together (can be placed in a shell script):
UPDATE_LIST=$( java -jar /root/jenkins-cli.jar -s http://127.0.0.1:8080/ list-plugins | grep -e ')$' | awk '{ print $1 }' );
if [ ! -z "${UPDATE_LIST}" ]; then
echo Updating Jenkins Plugins: ${UPDATE_LIST};
java -jar /root/jenkins-cli.jar -s http://127.0.0.1:8080/ install-plugin ${UPDATE_LIST};
java -jar /root/jenkins-cli.jar -s http://127.0.0.1:8080/ safe-restart;
fi