Server-side Web applications are constantly exposed to new threats as new technologies emerge. For instance, forced browsing attacks exploit incomplete access-control enforcement to perform security-sensitive operations (such as database writes without proper permission) by invoking unintended program entry points. SQL command injection attacks (SQLCIA) have evolved into NoSQL command injection attacks targeting the increasingly popular NoSQL databases. They may expose internal data, bypass authentication or violate security and privacy properties. Preventing such Web attacks demands defensive programming techniques that require repetitive and error-prone manual coding and auditing. This dissertation presents three methods for improving the security of server-side Web applications against forced browsing and SQL/NoSQL command injection attacks. The first method finds incomplete access-control enforcement. It statically identifies access-control logic that mediates security-sensitive operations and finds missing access-control checks without an a priori specification of an access-control policy. Second, we design, implement and evaluate a static analysis and program transformation tool that finds access-control errors of omission and produces candidate repairs. Our third method dynamically identifies SQL/NoSQL command injection attacks. It computes shadow values for tracking user-injected values and then parses a shadow value along with the original database query in tandem with its shadow value to identify whether user-injected parts serve as code. Remediating Web vulnerabilities and blocking Web attacks are essential for improving Web application security. Automated security tools help developers remediate Web vulnerabilities and block Web attacks while minimizing error-prone human factors. This dissertation describes automated tools implementing the proposed ideas and explores their applications to real-world server-side Web applications. Automated security tools are effective for identifying server-side Web application security holes and a promising direction toward better server-side Web security. / text