How do I automatically set the version of my Inno Setup installer according to my application version?

You can use the Inno Setup Preprocessor GetVersionNumbersString function like this

#define ApplicationName 'Application Name'
#define ApplicationVersion GetVersionNumbersString('Application.exe')
[Setup]
AppName={#ApplicationName}
AppVerName={#ApplicationName} {#ApplicationVersion}
VersionInfoVersion={#ApplicationVersion}