How to define section parent page? I have a structure section with entry url format: "products/{slug}". 
All entries have they urls like "/products/category1/subcategory1/product1". 

Currently, I have a header navigation which opens product category pages like "products/category1".What is the preferred way to define "/product" page?
You have to select the "level" in the structure. Im guessing the products are always on level 4? If so you could try this:

{% set entries = craft.entries.section('yourSectionHandle').level(4) %}

{% for entry in entries %}
    ...
{% endfor %}