The Tibetan Plateau accommodated major upper crustal shortening during Indian Plate oceanic and continental lithosphere subduction. Deciphering whether shortening was continuous or episodic, and how it correlates to major geodynamic changes is challenging. Here we apply anisotropy of magnetic susceptibility (AMS), a sensitive synsedimentary strain indicator, to a ~3 km thick magnetostratigraphically dated sedimentary section (69–41.5 Ma) in eastern Tibet. AMS shows “earliest deformation” fabrics from 69–52 Ma, followed by a sudden change to “pencil structure” fabrics with increasing anisotropy degree at ~52 Ma, dating a sudden increased synsedimentary shortening strain. This change coincides with enhanced sedimentation rates and synsedimentary vertical‐axis rotations of the Gonjo Basin, suggesting a causal link to a marked India‐Asia convergence rate deceleration. We show that AMS analysis provides a strong tool to distinguish between climatic and tectonic causes of sedimentological change and is an asset in identifying discrete tectonic pulses in intensely deformed terrane.