Kali Linux is a popular operating system for conducting web application penetration testing because it comes pre-installed with a wide variety of tools for this purpose. Some popular tools that can be used for web application penetration testing on Kali Linux include:

1. Burp Suite: A comprehensive tool for performing web application security testing. It includes features such as intercepting proxy, spidering, and automated scanning.
2. sqlmap: A tool for detecting and exploiting SQL injection vulnerabilities in web applications.
3. OWASP ZAP: A tool for performing web application security testing, it includes features such as vulnerability scanning, spidering, and intercepting proxy.
4. Metasploit: An exploitation framework that can be used to exploit vulnerabilities in web applications.
5. Nmap: A tool for network discovery and security auditing that can also be used to identify open ports and services on a web server.

To use these tools for web application penetration testing, you will first need to identify the target web application. You can use tools such as Nmap or the browser’s developer tools to gather information such as the web application’s IP address, open ports, and technologies used.

Once you have identified the target web application, you can use the appropriate tools to conduct penetration testing. For example, you can use Burp Suite or OWASP ZAP to perform automated and manual testing of the application’s security.

You can also use sqlmap to test for SQL injection vulnerabilities, Metasploit to exploit any vulnerabilities found, and Nmap to check for open ports and services on the web server.

It’s worth mentioning that web application penetration testing should only be performed on applications that you have explicit permission to test, otherwise it is illegal. Also, the methodology and approach should be defined and followed, such as OWASP Testing Guide, PTES or NIST SP800-115.

Performing a penetration test on a web application using Kali Linux involves several steps and requires a combination of different tools. The general process for performing a penetration test on a web application using Kali Linux is:

1. Reconnaissance – Gather information about the target web application using tools such as Nmap, Whois, and Dnsenum. This information can be used to identify potential vulnerabilities and attack surfaces.
2. Scanning – Use tools such as Nessus, Nmap, and OpenVAS to scan the target web application for vulnerabilities. These tools can be used to identify known vulnerabilities, as well as misconfigurations and weak authentication mechanisms.
3. Exploitation – Attempt to exploit any vulnerabilities identified during the scanning phase using tools such as Metasploit, sqlmap, or Burp Suite. These tools can be used to gain unauthorized access to the web application, steal sensitive information, or execute arbitrary code.
4. Post-Exploitation – Attempt to gain persistence access and gather more information on the target web application and the organization behind it.
5. Reporting – Prepare a report that documents the testing methodology, findings, and recommendations for addressing any vulnerabilities or weaknesses identified during the test.

It is important to note that performing a penetration test on a web application without proper authorization is illegal in most jurisdictions. Additionally, performing a penetration test on a web application can put the security of the system or network at risk, so it should only be done with proper authorization and in a controlled environment. Also, it is important to use the latest version of the tools and keep up to date with the latest vulnerabilities and patches.