webpack.config.js

/* Load Zepto as module */
module.exports = {
    entry: "./app.js",
    output: {
        path: __dirname,
        filename: "bundle.js"
    },
    module: {
      loaders: [
        { test: /zepto(\.min)?\.js$/, loader: "exports?Zepto; delete window.$; delete window.Zepto;" },
      ]
    },
    resolve: {
      alias: {
        "zepto": "zepto/zepto.min.js",  // var $ = require('zepto')
        // "$$": "zepto/zepto.min.js",    // var $ = require('$')
      }
    }
};

This is super helpful; thanks! N.b., I had to remove the line in module.loaders to make this work with ts-loader!