I came across this problem myself when bundling with webpack and found the answer on this thread.
The way to solve it for me was to use the following config:
module.exports = {
entry: "./app",
output: {
path: __dirname,
filename: "bundle.js"
},
module: {
loaders: [
{
test: /\.js$/,
exclude: 'node_modules',
loader: 'babel',
query: {presets: ['es2015']},
}
]
},
target: 'node'
};
By setting target to node webpack will make the necessary changes to bundle your node application
Edit: This answer targeted webpack 1.x which has now been superseded.