Does Google put penalty for 404 : Not Found ?

I recently changed a URI structure at www.ionclerk.com network with over a hundred sites.
I realized I forgot to include proper redirection headers. Although that was solved less than 1 hours after the mishap happened. It was too late, I had 4000+ Page Not Found errors on my Google WMT dashboard. Now, its all fine but 'm stuck with the question "Does Google penalize sites for 404 ?

Generally, 404 errors don’t impact your site’s ranking in Google, and you can safely ignore them. Typically, they are caused by typos, misconfigurations (for example, for links that are automatically generated by a content management system) or by Google’s increased efforts to recognize and crawl links in embedded content such as JavaScript. - A page from Google Support