The combination of these two open-source platforms provide a robust, flexible and customizable eCommerce store solution.
Their popularity in the market has ensured the development community is regularly providing solutions and plugins for most required functionality for B2B and B2C companies.
Your choice of which platform to choose for your ecommerce store is often between WooCommerce (#1 in market share) Shopify (#2 in market share) and Magento (#3 in market share). 
All 3 are excellent solutions but they are not equal.
To decide which system is best for your business, consider the following:
Here is how WooCommerce compares to Shopify in each of these considerations
Features & Functions
Shopify is known for its simplicity of use and its minimal functionality. The WordPress/WooCommerce solution provides a mid-market solution in terms of functionality.
To extend their functionality both systems offer an abundance of third-party extensions. WordPress/WooCommerce call these extensions and plugins while Shopify calls them App’s. There is a much greater quantity of plug-ins available for WordPress/WooCommerce from the open-source community compared to the Shopify app store.
It is important to note that it is quite easy and cost effective to customize WordPress, WooCommerce and it’s plug-ins while Shopify and its apps can be difficult and expensive to customize.
Ease of Use & Implementation
Both of these solutions are considered easy to use for website administrators. Shopify gets slightly higher marks when only the base, native system is used. However, once many plugins are installed, some users complain that ease of use becomes increasingly more difficult and time consuming.
Implementing and setting up a WordPress/WooCommerce store requires more technical skills than a Shopify store. If the WooCommerce store has more features and functions it can also be more time consuming to implement.
Shopify takes care of the hosting and software updates.
Integrations
Integrations are an important component of a successful eCommerce initiative. This is where the eCommerce website communicates with your ERP, POS, CRM, accounting, and other platforms you use to run your business.
There are typically three methods for eCommerce website integrations:
- A “Bridge” software between the applications and your website
- Direct connect API’s (Application Protocol Interface)
- Data transfers through the FTP protocol
Both platforms provide a host of solutions for many popular 3rd party applications.
ROI & Costs
WordPress/WooCommerce is free open source solution. You might pay a one-time fee for plugins and a professionally designed theme, but these costs are usually nominal. Third party hosting will typically cost in the range of $25 to $200 per month. You will need to do updates either quarterly, semi-annually, or annually depending on your volume and complexity.
With Shopify, you pay a monthly hosting fee, transaction fees and possibly a percentage of your sales. The most expensive component for most small and mid-size Shopify implementations is their plugin/app fees. Most companies easily require a minimum of 5 to 10+ of these expensive plugins.
Payment Gateways Both WooCommerce and Shopify support many payment providers. The difference is Shopify encourages the use of their default payment gateway and charges a fee for using other options, which can be very costly but simpler to start with.
Search Engine Optimization (SEO)
SEO still ranks in the top 3 for recommended marketing solutions that produce an ROI for B2B and B2C eCommerce companies.
WordPress/WooCommerce overall is more effective and easier to encourage higher Google ranking, especially if you are trying to accomplish location-based SEO.