It's not exactly caching.
They use a script loaded on the webserver, which communicates with their edge server. When a dynamic page is requested, the script is able to tell what portions of the page are different, and pull only the unique content/changes from the host, and serves the rest from cache.
i.e. Let's say you have a page that is dynamic (un-cachable) but the only difference is "Welcome (username)" at the top. Cloudflare will serve the page from cache, and only pull the username from the host.
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