Little is known about the scale of natural variability of the Southern Hemisphere upper ocean on decadal to centennial time scales, despite its potential importance for influencing regions as distant as the tropical Pacific (El Niño–Southern Oscillation; ENSO) or even the North Atlantic overturning circulation. Here we present the first subdecadally sampled reconstruction of variability in the southeast Pacific upper-intermediate ocean from ca. A.D. 0–1300 using foraminiferal oxygen and carbon isotope records. Our results reveal large variability in surface ocean physical properties on both decadal and centennial time scales in the southeast Pacific; as much as 3 °C or more in as little as 50 yr. On centennial time scales, changes in Antarctic Intermediate Water physical properties (benthic foraminiferal δ18O) covary with those in the surface and are associated with shifts in tropical temperatures, thermocline nutrient dynamics, and ENSO, suggesting that they are part of a common Pacific-wide phenomenon. Our results reveal that natural variability in upper ocean properties is greater than previously appreciated and coherent with changes in the tropical thermocline, supporting both theories and models postulating the importance of extratropical-tropical teleconnections and the oceanic tunnel in interdecadal to centennial climate variability.