The Indonesian Throughflow (ITF) is a critical component of the global ocean overturning circulation and Indo-Pacific circulation. Climate models consistently project a weakening of the ITF during the 21^st century in response to greenhouse gas forcing. This centennial change has been linked to the weakening of the Atlantic Meridional Overturning Circulation (AMOC) as well as changes to surface winds over the Indo‐Pacific, but these processes are not enough to explain the magnitude of ITF weakening. Here, we show that changes to the Southern Ocean can explain the unresolved fraction of ITF weakening via process like the AMOC effects. We also propose a method to decompose the different contributions to the ITF weakening and find that combined AMOC and Southern Ocean explains, on average, 89% of the projected ITF decline in climate models. Our results highlight the crucial role of bipolar processes in modulating Indo-Pacific low‐latitude ocean circulation variability under a changing climate.