The writing has been on the wall for a LONG time now, actually. Starting with (IIRC) Leopard, iCal began using the Helvetica font; Address Book/Contacts had Helvetica since at least Snow Leopard, and Dashboard in Tiger had Helvetica used in the widgets. So, for a long time now, Helvetica has been used sparingly within OS X. I think it was around Snow Leopard/Lion when Helvetica became a bit more prominent, though. That's something Apple does - gradually introduce something new, use it more and more, then introduce it full-on.
We're at that point now, where Helvetica is the primary system font.
As to how to change it - I'm not sure. I'm sure someone ingenious will find a hack to change the system font, but even so, it's not guaranteed to be completely seamless.