The mid to late Pliocene (~4.2–2.8 Ma.) represents an experiment in climate sensitivity to orbital pacing in which nearly all continental ice was confined to the Southern Hemisphere. Most studies have emphasized the dominant role of obliquity in determining changes in ice volume and temperature at this time, although most records come from the Northern Hemisphere, instead of the hemisphere where the bulk of ice resided. We present the first orbitally‐resolved, mid to late Pliocene Southern Hemisphere paired records of surface and subsurface variability from two deep ocean archives from the Southwest Pacific Ocean (Sites 594 and 1125). These records indicate dominance of low frequencies centered at ~100 kyr for this time period. Because these signatures extend coherently and synchronously from middepth water properties (δ13C, δ18O of benthic foraminifera), which have their chemistry set in the subantarctic belt, to the surface (alkenone‐derived surface temperature estimates, color reflectance, and magnetic susceptibility), we infer that the fingerprint of the ~100‐kyr cycles must have extended over a large region of the Southern Hemisphere. We propose that nonlinearities in climate response to precessional forcing—most likely through ice sheet and/or carbon cycle behavior—generated the observed low frequency. A review of published mid to late Pliocene time series suggests that the ~100‐kyr pacing may be a widespread phenomenon and that major approximately 100‐kyr excursions in Pliocene climate were an important overlay to the underlying 41‐kyr glacial‐interglacial rhythm. These results caution against uncritical use of existing Pliocene isotopic templates to construct high‐resolution age models.