Equatorial Southeast Asia is a key region for global climate change. Here, the Indo-Pacific Warm Pool (IPWP) is a critical driver of atmospheric convection that plays a dominant role in global atmospheric circulation. However, fluctuating sea-levels during the Pleistocene produced the most drastic land-sea area changes on Earth, with the now-drowned continent of Sundaland being exposed as a contiguous landmass for most of the past 2 million years. How vegetation responded to changes in rainfall that resulted from changing shelf exposure and glacial boundary conditions in Sundaland remains poorly understood. Here we use the stable carbon isotope composition (δ13C) of bat guano and High Molecular Weight n-alkanes, from Saleh Cave in southern Borneo to demonstrate that open vegetation existed during much the past 40,000 yrs BP. This location is at the southern equatorial end of a hypothesized 'savanna corridor' and the results provide the strongest evidence yet for its existence. The corridor would have operated as a barrier to east-west dispersal of rainforest species, and a conduit for north-south dispersal of savanna species at times of lowered sea level, explaining many modern biogeographic patterns. The Saleh Cave record also exhibits a strong correspondence with insolation and sea surface temperatures of the IPWP, suggesting a strong sensitivity of vegetation to tropical climate change on glacial/interglacial timeframes.