As noted several times throughout the series, her body is, in fact, a doll.
Though I seem to remember it being noted earlier, the first mention I can find is the very first line spoken in Tsukimonogatari:
Ononoki Yotsugi is a doll.
I am not aware of any reason to believe this is meant to be taken metaphorically. That this isn't obvious from the anime visuals--aside from her trademark lack of facial expression--is inconsequential. In Koyomimonogatari, she herself attributes her height to being "by nature, an adorable doll".
If you're wondering how, in that case, she could be mistaken for human, an adequately realistic doll would not look glaringly inhuman from a distance, and even close up it may not be clear without deliberate inspection. In Owarimonogatari:
It is revealed that Teori Tadatsuru, one of her creators, was himself possessing a doll during the events of Tsukimonogatari. As Araragi was disturbed by having seen "the cute doll known as Ononoki Yotsugi murder a human", he at no point discerned that his body was that of a doll. So it is generally possible for supernaturally-animated dolls, at least those created by Teori, to pass as human. (Interestingly, here there are also several shots of dolls in Ononoki's likeness, except with visible ball joints.)
And as for why Tsukihi unambiguously perceives her as a doll, if you won a doll from a claw game (as noted but 30 seconds before the line cited in the question), saw it up close, felt it, and never saw it do anything but hang limp, what reason would there be to doubt that it is in fact a doll?