We present a precisely dated, multi-proxy stalagmite record from Liang Luar Cave, Flores (southeast Indonesia) that reveals a rapid increase in Indonesian monsoon rainfall at ~9.5ka. A "ramp-fitting" method for detecting statistically significant inflections in a time-series was applied to the stalagmite δ18O, Mg/Ca, and Sr/Ca profiles to quantify the precise timing and magnitude of an abrupt increase in monsoon strength over a period of ~350years. Previously published lake-level records from the monsoon-affected Australian interior show a sudden intensification of the Australian monsoon at ~14ka. However, our records indicate that monsoon intensification in Flores occured ~4-5kyr later. The timing of the monsoon shift in Flores is synchronous with the rapid expansion of rainforest in northeast Australia and regional freshening of the southern Makassar Strait which, under present-day conditions, is sensitive to monsoon variability. The freshening of southern Makassar was coeval with an abrupt ~1.5°C cooling in the upper thermocline of the Timor Sea ~9.5ka, indicative of reduced surface heat transport by the Indonesian Throughflow (ITF) when the Java Sea opened during postglacial sea-level rise. This suggests that the abrupt increase in monsoon rainfall on Flores was not due to a change in the ITF - because a decrease in rainfall would be expected to accompany cooler local sea surface temperatures (SSTs) - but rather by the sudden increase in ocean surface area and/or temperature in the monsoon source region as the Sunda Shelf flooded during deglaciation. We propose that it was the abrupt intensification of the monsoon through the late deglaciation that maintained the subsequent structure of the ITF following the flooding of the Sunda Shelf at ~9.5ka. © 2012.