Final answer:
The best security measure to secure the web server until the replacement is ready is an application firewall, as it provides protection without affecting the existing application.
Step-by-step explanation:
A recent penetration test has identified a major vulnerability in a web server that requires 99.99% availability and currently hosts a critical shipping application. This application is set to be replaced in three months, and attempting to fix the vulnerability may disrupt the application's operation. Given these constraints, the most appropriate course of action to secure the web server until the new system is deployed would be to implement an application firewall.
An application firewall would act as an intermediary, inspecting incoming traffic and applying rules to prevent exploitation of the identified vulnerability without necessitating changes to the application itself. This solution avoids the risks associated with patch management, does not rely on signature-based defense like antivirus, and is more tailored to web traffic than a Host Intrusion Detection System (HIDS) or spam filters.