Unlike other rauisuchians, which have a prominent ridge on the ilium called the supra-acetabular buttress that overlies the femur, Stagonosuchus possesses only a slight thickening on the surface of the bone.

[1][2] In Stagonosuchus, the pubis is broad and plate like, while in other genera it is narrower and may have a prominent "foot" like that of some theropod dinosaurs.

In the vertebrae, the neural canals (through which the spinal cord would pass) extend into the centra, forming deep concavities.

[4] A wide articulation between the hyposphene and hypantrum in successive vertebrae prevented any lateral movement of the spine.

A 2010 study on archosaurian phylogeny found Stagonosuchus to be outside both Rauisuchidae and Prestosuchidae in a more basal position within Rauisuchia.