The punctuated distribution of major gold deposits along orogenic belts is poorly understood. In northern Perú, gold deposits cluster along trends that transect the subparallel Phanerozoic belts that accreted onto the western margin of the Archean–Proterozoic Amazonian craton. This suggests the influence of as yet unrecognized pre-Andean basement structures in controlling the localization of Phanerozoic deposits. We report the newly discovered Tomac ophiolite, which represents a missing link in tracing a cryptic basement collisional suture striking obliquely to the Peruvian Andes. The Tomac ophiolite signals the opening of a former Neoproterozoic ocean basin between the Amazonian craton and a continental ribbon of dispersed microterranes. Re-accretion of the continental ribbon resulted in the formation of a collisional belt between ca. 465 and 440 Ma. Rifting and re-accretion occurred parallel to the strike of the ca. 1400–1000 Ma Grenvillian-Sunsás orogen, indicating that structural corridors that transect the Andes at an oblique strike angle reflect inheritance of preexisting lithospheric weak zones. Our study demonstrates that Phanerozoic gold deposits in northern Perú cluster at the intersection between the newly defined basement suture and the superimposed Andean belt and associated well-documented cross faults.