A method and system for automating application of software patches to a server system having a virtualization layer. A plurality of software patches are downloaded to a computer system having a first operating system. The software patches to apply to a server console operating system are then determined. The software patches are automatically copied to the server system by executing a first script file. The copied software patches are automatically decompressed by executing a second script file. The decompressed software patches are installed in a specified order by executing the second script file. The console operating system is rebooted only after all software patches are installed.