The East Gondwana was formed by the assembly of continental fragments, namely India, Madagascar, Sri Lanka, and Antarctica, with the evolution of 2000 km long East African Orogen around 550 Ma. Lack of knowledge on the subsurface structure of the orogen led to a wide range of evolutionary models. The present study attempts to resolve various models’ ambiguity by presenting new results of the first deep seismic reflection study across the Achankovil Shear Zone, Southern Granulite Terrain, India that was evolved during the East African Orogen. The seismic study is also the first of its kind among the east Gondwana fragments. The Common reflection surface stack images of the present study reveal hitherto unknown details along with a unique south-dipping reflection fabric extending from the surface to upper mantle depth. We interpret this fabric is formed due to subduction-accretion of Madurai and Trivandrum blocks during the East African Orogen and represents a suture zone. Two deep-seated shear zones, the Achankovil and Tenmalai were also developed at both ends of collision fabric with strike-slip characteristics. Orogenic collapse and post-orogenic extension are inferred from the subhorizontal lower-crustal reflection fabric, which is interpreted as an equilibrated younger Moho. The present study provided an opportunity to understand the formation and exhumation of granulites, which act as a window on the inaccessible lower continental crust. Gravity modelling is performed along the seismic profile. Integration of present results with the existing geological and geophysical data provided basic constraints on the structure and tectonics of east Gondwana fragments and the East African Orogen.