You pay for them.

The only exception: if you fly so much* on Air France and KLM (it has to be these 2 airlines) that you obtain "Ultimate" status, and then you get a limited number (4?) of upgrade vouchers, each one good for a single-cabin upgrade (so: Y to J on an AF widebody would require 2 vouchers).

*you need to earn 900 XP on AF and/or KL flights in your qualification year to get "Ultimate" status. That's the same number of XPs are as required to qualiify from Gold to Platinum 3 times over.