We report the last glacial-interglacial transition of marine denitrification off northern Chile based on sedimentary nitrogen isotopes. Our results show a relatively early, large and abrupt transition from low to high denitrification regimes consistent with recently-reported data from off Peru. The deglaciation is characterized by millennial-scale adjustments of the oxygen minimum zone that mimic the atmospheric temperature record from Antarctica. We also show that the sharp denitrification onset was not caused by an increase in local primary productivity, nor by ventilation changes occurring in the Southern Ocean, as previously proposed. We found that the magnitude and timing of the deglacial denitrification changes are in close agreement with the fresh-water pulses that resulted from the melting of the Patagonian Ice Sheet. We consequently attribute the deglacial onset of marine denitrification in the area to a collapse of the thermocline ventilation occurred at the mid-latitude subduction region of the eastern South Pacific.