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Showrunner Steven Moffat confirmed at a press screening that Matt Smith's Time Lord will then be joined by "a new friend", who has yet to be cast.
"The final days of the Ponds are coming during the next series," he said. "I'm not telling you when or how, but that story is going to come to a heartbreaking end... Then The Doctor will meet a new friend."
Moffat added that he believes River Song (Alex Kingston) will make a return appearance, though it is unknown if the character will be involved in the couple's exit storyline.
It has been announced on the official Doctor Who Twitter profile that more details will be revealed tomorrow (December 16).
Smith stated: "The show will miss the Ponds, brilliantly played by Karen and Arthur, but the great thing about Doctor Who is its ability to change.
"We had the most incredible journey. We took over the show and we've really had to hold hands and help each other through it.
"So it's very disappointing, but one has to remember that this show is about change and regeneration, and that's what galvanizes it and pushes it forwards."
Gillan and Darvill both made their Doctor Who debut as Amy and Rory in the first episode of the show's fifth series in 2010.
Watch a video of Amy and Rory's wedding party from the end of series five below: