When and How was Homura's wish fulfilled? In ep. 10, Homura's wish is revelaed:


   "I want to redo my meeting with Kaname-san. Instead of being protected by her, I want to protect her!" 


This wish forced her to go back in time and re-live the month since her meeting with Madoka 100-ish times.

But in the end of the main timeline (ep.12), it is still Madoka that saves the day 


   by wishing to rescue all magic girls before they "completely" turn into witches.


Since the world was rebooted by Madoka's wish we briefly see events that happened during that month, such as


   Sayaka's despair for being unable be with Kamijou, only to be rescued by Madoka.


I won't address the Rebellion movie in this question body, but feel free to include it in the answers.

Since by the end of ep.12 it does not feel like Homura's wish was fulfilled, question remains:

Was it fulfilled, if yes, when and how?
If you are referring to how Homura can still have her wish granted in Madoka's Universe, one reason could be, as Euphoric said, it's a paradox. but then again we can say that for anything, it's more fun to see what we can infer from what we have seen, isn't it?

The second could be what I am going to call the Room of Origin (my term, not canon, since it has no name to my knowledge). We see the Room or Origin twice as being the center point of the universe being created. the first time was when Madoka recreated the universe and the second time was when Homura did it at the end of Rebellion (in Rebellion Homura says she's been there once before when the Incubator asks where they were). Since this is really ground zero for the start of the new universe we can make the assumption that a part of the old universe still exists inside the Room or Origin, serving as the basis.

The third reason could be that Homura retained her memories and abilities because she was key to creating Madoka's Universe. It was her terminating the timelines that compiles Madoka's Karmic Destiny that allowed her to become a god. In Homura's Universe Madoka regaining her memories would return her to becoming the full Law of Cycles once more and Sayaka retaining her memories initially could be because she is a part of the Law of Cycles as her secretary until Homura sealed them and probably sealed Nagisa before hand (since she did create a new life for Nagisa)