You don’t need any special permission to use San Francisco on your web site. But to be precise, you can’t use “San Francisco”. In your CSS, you can specify “-apple-system” and the font-family. On systems that have San Francisco installed, then your text should show up in that typeface. You would need to specify one or more fallback typefaces for those systems that do not have San Francisco installed. However, macOS 10.15 could change the system typeface and then you might have various display problems. You could have display problems regardless. The system font is not designed for use on web pages. You could use characters that don’t exist in that typeface.
I can tell you with certainty that you may not distribute the San Francisco font in any way.
In the end, it would probably be a better idea to just use a standard typeface or use your own web font for which you have rights.