Apple EarPods are not compatible with 3rd gen iPod shuffle. The product listing at Apple for the EarPods
http://www.apple.com/shop/product/MD827LL/A/apple-earpods-with-remote-and-mic
only lists the 4th gen shuffle under Compatibility. The previous Apple "Earphones" do work with 3rd gen shuffle, as noted in this document
Compatibility of Apple wired headset models with iPhone, iPad, and iPod models - Apple Support
You may be able to find the older version online or in stock at retailers.
As an alternative, you can buy an "adapter" that has the playback control buttons. For example
http://www.amazon.com/Griffin-Headphone-Control-Adapter-iPod/dp/B003A5AXP4
There are other similar products, but I use this one as the example because the description specifically says, "Fully compatible with iPod shuffle (3rd generation)." With an adapter, you can connect any standard headphones, including the EarPods.