On Certbot's side there is no problem. Just request a certificate for each domain and Certbot will renew them automatically.
Since Apache 2.4 supports Server Name Indication, there is no problem on this side either. You just need to configure a different certificate for each virtual host:
<VirtualHost *:443>
ServerName example.com
SSLEngine on
SSLCertificateFile /etc/letsencrypt/live/example.com/fullchain.pem
SSLCertificateKeyFile /etc/letsencrypt/live/example.com/privkey.pem
</VirtualHost>
<VirtualHost *:443>
ServerName example.net
SSLEngine on
SSLCertificateFile /etc/letsencrypt/live/example.net/fullchain.pem
SSLCertificateKeyFile /etc/letsencrypt/live/example.net/privkey.pem
</VirtualHost>
Edit: If you don't want certbot to mangle with your Apache configuration, use the webroot plugin. Create a directory for certbot:
mkdir -p /var/www/certbot/.well-known/acme-challenge
Add an alias to all your <VirtualHost>
's running on port 80 or globally:
Alias "/.well-known/acme-challenge/" "/var/www/certbot/.well-known/acme-challenge/""
Run cerbot with the webroot plugin:
certbot certonly --webroot -w /var/www/certbot -d example.com -d www.example.com
Certbot will remember those settings, when renewing the certificates.