The Pliocene-Pleistocene transition marks a fundamental reorganization of Pacific dynamics, yet the impact on the faunal communities of the Southeastern Pacific (SEP) remains poorly constrained. Utilizing PCA and diversity indices derived from planktic foraminiferal census data at ODP Site 1236, we observed a profound transition from an ecological optimum to a state of critical ecological constriction. This initial optimum (~3.5 Ma) was sustained by a bathymetrically expanded mesopelagic niche, which underwent a systemic decline in species richness and evenness as integrated tectonic and climatic forcing, linked to the Central American Seaway closure, drove the ecosystem toward a critical tipping point by ~2.9 Ma. We further demonstrate that the intensification of the Southeast Trade Winds and subsequent wind-driven upwelling, contemporaneous with the onset of the Northern Hemisphere Glaciation, accelerated the vertical compression of the subsurface habitat to an absolute ecological minimum at ~2.55 Ma. The SEP hydrographic reorganization provides a direct ecological expression of shifting global boundary conditions, linking high-latitude cooling to the definitive establishment of the vertically integrated Pleistocene East Pacific upwelling system.