Oblique dextral motion on the central Alpine Fault in the last circa 5 Ma has exhumed garnet-oligoclase facies mylonitic fault rocks from ∼35 km depth. During exhumation, deformation, accompanied by fluid infiltration, has generated complex lithological variations in fault-related rocks retrieved during Deep Fault Drilling Project (DFDP-1) drilling at Gaunt Creek, South Island, New Zealand. Lithological, geochemical, and mineralogical results reveal that the fault comprises a core of highly comminuted cataclasites and fault gouges bounded by a damage zone containing cataclasites, protocataclasites, and fractured mylonites. The fault core-alteration zone extends ∼20–30 m from the principal slip zone (PSZ) and is characterized by alteration of primary phases to phyllosilicate minerals. Alteration associated with distinct mineral phases occurred proximal the brittle-to-plastic transition (T ≤ 300–400°C, 6–10 km depth) and at shallow depths (T = 20–150°C, 0–3 km depth). Within the fault core-alteration zone, fractures have been sealed by precipitation of calcite and phyllosilicates. This sealing has decreased fault normal permeability and increased rock mass competency, potentially promoting interseismic strain buildup.