In the latest version of Chrome Canary 41.0.2270.0 a new flag is available - Enable Extension Toolbar Redesign. I believe this has been available for a while on Windows/Linux but it is now available for Chrome on OS X.
The flag is available at:
Once enabled all extension icons are removed from the Chrome toolbar and are moved to the dropdown box that is launched when pressing the burger menu located at the end of the Chrome Omnibox.
It looks a bit ugly so I hope there will be some improvements on it in future updates.
You can still drag the edge of the Omnibox to show extension icons in the extension toolbar, this is just a better way of hiding the icons so you still have quick and easy access to them.