DON'T TRUST SITE OR MALWARE SCANNERS!
You should use a firewall extension like Admin Tools to secure your cms. Unfortunately it's a bad practice to try to get your infected site back online, yeah because it's compromised and could have some backdoors now.
The best and secure way would be setting up a new Joomla site and transferring your content by hand from your old site.
But, what I do in such situations:
Make a list of installed third-party extensions (plugins,
modules, components). Deactivate ALL OF THEM.
Duplicate the current database to a new one. (Databases should always have limited local access, no remote access! Don't use the old database password!)
Setup a new Joomla installation, after the installation change
the database to the duplicated one. This can lead to some errors if
your database is from a different Joomla version. Reinstall the last
Joomla update via com_joomlaupdate (?option=com_joomlaupdate), if
necessary do a database repair run through the com_installer
Reinstall your third-party extensions (latest version) and
activate them one by one.
If possible, install a fresh and updated version of your frontend
template. If it's custom or modified and you are familiar with PHP
/ JS and malware code, you can download your old template via FTP and
check every file (php,js,css etc.) for malware code, remove it. Zip
your template and install your template to the new site.
Install and setup Admin Tools firewall.
Check every third-party extension if they are really needed, if
not, uninstall them. Mostly your form extensions or extensions with
ajax calls are the weak point.
If possible, get a SSL-certificate (Let's Encrypt e.g.) and force
SSL (Joomla config, htaccess) on your whole site.
Don't forget to change all user account passwords, your ftp
passwords and email passwords.
Delete all the data (ftp + database) from the old site and check if
there are more folders and files in the webspace root, those could
be also compromised and should be deleted or at least set chmod to
000 to lock access to those files and folders. (not your new installation of course)
Now you can start to unlist your domain from blacklists. Btw., always keep an eye on the folder and file permissions, NEVER use chmod 777!! (Admin Tools will handle this for you.)
Folders: 755 or "lower"
Files: 644 or "lower"
Do backups every week or month. (Akeeba Backup is good for me.)