Topological insulators (TIs) hold great promise for realizing zero-energy Majorana states in solid-state systems. Recently, several groups reported experimental data suggesting that signatures of Majorana modes in topological insulator Josephson junctions (TIJJs) have -- indeed -- been observed. To verify this claim, one needs to study the topological properties of low-energy Andreev-bound states (ABS) in TIs of which the Majorana modes are a special case. It has been shown theoretically that topologically non-trivial low-energy ABS are also present in TIJJs with doped topological insulators up to some critical level of doping at which the system undergoes a topological phase transition. Here, we present first experimental evidence for this topological transition in the bulk band of a doped TI. Our theoretical calculations, and numerical modeling link abrupt changes in the critical current of top-gated TIJJs to moving the chemical potential in the charge-accumulation region on the surface of the doped TI across a band-inversion point. We demonstrate that the critical-current changes originate from a shift of the spatial location of low-energy ABS from the surface to the boundary between topologically-trivial and band-inverted regions after the transition. The appearance of a decay channel for surface ABS is related to the vanishing of the band effective mass in the bulk and thus exemplifies the topological character of surface ABS as boundary modes. Importantly, the mechanism suggest a means of manipulating Majorana modes in future experiments.