As River Song explained immediately after it happened, 'Whatever that was, it killed him in the middle of his regeneration cycle. His body was already dead. He didn't make it to the next one.' the Doctor has mentioned before that he can be killed during the regeneration process, and we've seen it confirmed in an aborted timeline.
Furthermore, it was revealed in "The Wedding of River Song", that it was the Teselecta who was shot, and not the Doctor, and the apparent aborted regeneration was just a light show.