A method of manufacture of an integrated circuit packaging system includes: providing an integrated circuit substrate having a non-active side and an active side; forming a recess in the integrated circuit substrate from the non-active side exposing a first contact and a second contact with the first contact and the second contact along the active side; forming a first via, having a first via extension extended beyond the non-active side and an opening at the non-active side, within the recess; forming a barrier liner within the opening with the barrier liner exposed beyond the non-active side; and forming a second via over the barrier liner and within the opening of the first via with the second via exposed beyond the non-active side.