One embodiment of the system disclosed herein facilitates identifying a system call in an application and replacing the identified system call with a customized function call. During operation, the system executes an executable file of the application, wherein the executable file has been modified to execute a hooking and injection manager at run time. Prior to executing the system call, the system executes the hooking and injection manager. While executing the hooking and injection manager, the system determines, from a symbol table, a symbol table index value corresponding to a symbol associated with the system call. The system further determines an import table entry storing a pointer to the system call based on the symbol table index value, and changes the pointer in the import table entry so that the pointer indicates an address of the customized function call.