Google Webmaster Tools is a collection of utilities from Google that help site owners improve their website visibility. To use these tools with Cloudflare, users can verify ownership of the site through the Cloudflare Apps page. Once verified, users can enable features like Always Online, which caches a subset of pages for display when the origin server is offline. The process involves signing in to Google from the Cloudflare Apps page and following a link to Google Webmaster Tools for verification.