Sherlock did call Mycroft in "The Hounds of Baskerville" and I'm pretty sure he made at least one phone call to Lestrade in "The Great Game". However, I don't think he's ever phoned John before this episode, so I suppose that could be it...But didn't Sherlock have an actual conversation with John in which he responded to things John said? And that did look like Sherlock standing on top of the building and speaking into the phone. I'll have to rewatch the scene -- something I keep saying, I know.