Is there a user font for San Francisco in El Capitan?

They are System fonts & not available (or indeed licensed) for documents that you make or App use in general.
As mentioned in comments, even the developer version of the fonts is only licensed for interface mockups & no other purpose.

The previous system font, Helvetica Neue, on the other hand, was released as both a System & User font.

There are various opinions online about how to make the San Fransisco fonts available to the user, but seem to depend on unpacking the individual ttfs, changing the 'system font' attribute, then repacking them again - something I'll leave to someone else, regardless of the licensing or legal position of doing that.

Actually, just convert all the SFNS*.otf font in /System/Library/Fonts/ to ttf and install them to ~/Library/Fonts/. That will work fine.

EDIT : Apparently, it's working only for Pages, Keynote and Numbers under the name "System Font". Can't get it to work on other programs.

As San Francisco fonts are restricted for the developers to create mockups of interfaces, you can use similar fonts to San Francisco:

• Futura
• Roboto Sans

Tip: Try to mix the letters of both the fonts.