To send PDF files from Safari to the Documents app, follow the steps below:
Note: to troubleshoot the cases when Documents does not appear in the list of extensions, please see the following article (6.5. There is no Documents app in the 'Open in' menu).
Note: to open a file from Documents using the URI scheme in Safari, type rdocs:///folder/subfolder/file.pdf to open file.pdf stored in a folder/subfolder in the Documents tab within the Documents app.
In the Documents app, you can use the built-in browser to save a web page as a PDF file by tapping the Share button and saving the page as an HTML document, a PDF or a Web Archive. For more detailed information about the built-in browser, please check out the article here.