Entity reference autocomplete field node
First, to handle multi value fields you'll need this patch: https://www.drupal.org/node/2224803#comment-11477609

Second, depending on what Widget you have selected for your Entity Reference field, this does/can change what Services expects to be POST/PUT up to the server.

I personally always set the Widget as an Autocomplete, and then this JSON format is the correct one to use:

var node = {
  type: 'article',
  title: 'Hello world',
  language: 'und',
  field_foo: {
    und: [
      { target_id: '... (123)' }
    ]
  }
};


You can literally put anything you want in the position of the ..., the only thing that matters is the Entity ID is wrapped in the parenthesis.