In a standard fight, Doom wins. But I think if you take character traits into account, I think Doom takes a regeneration, then once he witnesses regeneration he tries to capture The Doctor, not allowing him to die until he figures out the secret. This gives The Doctor enough time to get out of there, maybe stopping Doom as well. Doom is too arrogant to believe anyone's planning skills are in the same neighborhood as his, and The Doctor's definitely are.