We discuss the phase structure of N D4 branes wrapped on a temporal (Euclidean) and a spatial circle, in terms of the near-horizon geometries. This system has been studied previously to understand four dimensional pure SU(N) Yang-Mills theory (YM4) through holography. In the usual treatment of the subject, the phase transition between the solitonic D4 brane and the black D4 brane is interpreted as the strong coupling continuation of the confinement/deconfinement transition in YM4. We show that this interpretation is not valid, since the black D4 brane and the deconfinement phase of YM4 have different realizations of the Z N centre symmetry and cannot be identified. We propose an alternative gravity dual of the confinement/deconfinement transition in terms of a Gregory-Laflamme transition of the soliton in the IIB frame, where the strong coupling continuation of the deconfinement phase of YM4 is a localized D3 soliton. Our proposal offers a new explanation of several aspects of the thermodynamics of holographic QCD. As an example, we show a new mechanism of chiral symmetry restoration in the Sakai-Sugimoto model. The issues discussed in this paper pertain to gravity duals of non-supersymmetric gauge theories in general.