Since the Doctor knew he was going to regenerate in this scene, and he also looked young-looking, I think we can presume the Doctor made this call in between the following two scenes in "The Time of the Doctor":
- The scene where a very elderly-looking Eleventh Doctor suddenly realized he had another regeneration and used the regeneration energy to blast the Daleks:
DALEK: The rules of regeneration are known. You have expended all your
DOCTOR: Sorry, what did you say? Did you mention the rules? Now,
listen. Bit of advice. Tell me the truth if you think you know it. Lay
down the law if you're feeling brave. But, Daleks, never, ever tell me
DALEK : Emergency! Emergency! The Doctor is regenerating! The Doctor
DOCTOR: Oh, look at this. Regeneration number thirteen. We're breaking
some serious science here, boys. I tell you what, it's going to be a
DALEK: Exterminate! Exterminate the Doctor.
DOCTOR: You think you can stop me now, Daleks? If you want my life,
ha, ha, come and get it!
- The following scene at the end of the episode, where Clara entered the TARDIS and found a young-looking Eleventh Doctor waiting for her, who explained his youthful appearance as a "reset" immediately prior to regeneration:
CLARA: You're young again. You're okay. You didn't even change your
DOCTOR: Ha! It's started. I can't stop it now. This is just the reset.
A whole new regeneration cycle. Ooo.
Also, you mention that in the phone call in "Deep Breath" we see a shot of Clara replacing the hanging phone on the TARDIS, a shot originally from "The Time of the Doctor"--and this scene did indeed happen between the two scenes I mentioned above, it's at 58:35 on the US blu ray (might be a little different on blu rays from other regions since the US blu ray is slowed down to 24 frames per second, whereas the episode was broadcast at 25 frames per second, a speed US televisions aren't designed to play).