According to the documentation, you can have Closure Compiler add the sourceMappingURL to the bottom of the script with something like this:

--output_wrapper "%output%
//# sourceMappingURL=output.js.map"

being added to your call. Not that you cannot use "\n" here, and you need a newline literal. On a Linux shell this works just fine (if you're inside of quotes when you press enter, the command doesn't get executed).