Download desired version (Hint: only select necessary languages)
https://download.dokuwiki.org

Create a backup:
tar zcpfv /web/backup/dokuwiki-200825.tar.gz /web/www/kb

Extract the new version:
tar xzvf dokuwiki-919579ec6e60818f9f712747c2b681d6.tgz

Copy new files:
rsync -avh /tmp/dokuwiki/ /web/www/kb

Restore ownership (on Debian):
chown -R www-data:www-data /web/www/kb

Optionally remove files which are not needed anymore:
grep -Ev '^($|#)' /web/www/kb/data/deleted.files | xargs -n 1 rm -rf

Upgrade templates and plugins if necessary