Against the South part of the Enclosure wall and immediately facing the Entrance Hall, a wall, forming an angular projection into the South Court, was decorated with recessed panels, topped by small drums, suggesting rolled reed-mats, and a frieze of uraei.
On its North face, a small entrance can be found.
Behind it a long, narrow mastaba, built directly against the inside of the Enclosure wall, was constructed above a shaft of 7 by 7 metres and 28 metres deep.
At the bottom of this shaft, a second burial vault, similar to that found underneath the pyramid, was constructed. With its 1.6 by 1.6 metres and a height of a mere 1.3 metres, it was much smaller than the pyramid's vault and too small for a human burial.
Other features of the pyramid's substructure had been replicated as well: a descending passage with stairs, starting in the West underneath the mastaba, and the inner chambers, tiled with blue faience.
The mastaba's substructure, however, was less complex, more complete and less damaged, which has been of some help in the restoration of the pyramid's substructure.
About halfway the descending passage, a magazine of 18 by 1.6 metres was found to contain some large jars, that may have contained food offerings. On top of these, a wooden stretcher, a box and posts form a baldachin had been left.
The passage leads further down to a set of chambers, most of which had inlaid faience tiles. In the South wall of Chamber II, located to the South-East of the burial vault, three false doors showing Netjerikhet, were carved.
The function and purpose of this South Tomb, that would continue on in pyramid building as the Satellite pyramid, usually built to the South of the main pyramid, are still not fully explained. It is clear that it can not have been intended as a burial place for the royal remains: the burial vault is too small to have contained the remains of an adult human being. The South Tomb of the unfinished pyramid complex of Sekhemkhet, Netjerikhet's successor, was found to contain the skeletal remains of a 2-year old child, that could not have belonged to Sekhemkhet himself because he ruled for 6 years.
The stone jars and the wooden stretcher found inside of the South Tomb of Netjerikhet, however, suggest that something was placed inside the tomb and that some offerings may have been made to whatever it was that was buried here.
One theory, supported by evidence found in the Satellite pyramids of later funerary complexes, explains this South Tomb as the burial place of the Ka of the king, probably embodied by a statue that was laid to rest inside the vault.