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So you want to automatically fill in the entity reference field on a newly created node with a reference to a node which is dynamically created 'after saving content', huh?
Modules used: entity reference and rules in Drupal 7. (basic sandbox setup)
So beneath the steps in your rule.
1. After saving new content of type 'story'
2. Create a new entity
Parameter: Entity type: Node, Content type: article, Title: article related to nid..., Author: 2
Provides variables: Created article (article_created)
3. Save entity
Parameter: Entity: [article-created], Force saving immediately: true
4. Set a data value
Parameter: Data: [node:field-myref], Value: [article-created]
Before you execute this rule, though, you should create an article node (I called mine 'a generic article') that you are going to use as the initial value set in the entity reference field of the node you're about to create.
Once you've created that generic article, go to the manage fields tab of the story content type and select 'a generic article' as the default value. That way, the entity reference field is set initially after the 'save entity' action and the 'set data value' action can take place.