Running ts-loader before babel-loader will do the trick.
Specifying that you want declaration files in config is all you need.
If you are using an absolute path, the output d.ts files will also contain absolute paths which are useless and will result in typescript compilation errors.
To fix that, I wrote a plugin to convert an absolute path to a relative path:
https://github.com/stavalfi/babel-plugin-module-resolver-loader