What is the most effective way to block IP address in Application Layer?

I understand that most Routers/Firewalls are able to block IP tables in the network level. IPtables for instance is quite effective.

However, I want an application layer IP block.I have an HAproxy load balancer that load balances traffic to 4 backend apache/nginx web servers. I sometimes encounter scraping and GET request DDoS on my website. I want to be able to quickly(manually) block IP address on the application layer. How do I block an IP address, Apache Allow/Deny, .httaccess? Is there a more effective/easier way to block the IPs? What if I have a huge list to block? I would also appreciate a way of blocking specific. User Agents.