Members of this group were lightly-built and moderately-sized reptiles. They do not show any adaptations for bipedalism, which became much more common in other avemetatarsalians. In addition, their leg proportions indicate that they were not capable of sustained running, meaning that they were also slow by avemetatarsalian standards.
Very little skull material is known for the group as a whole. The only skull bones which can be confidently referred to this group consist of a few pterygoid and postorbital fragments belonging to Yarasuchus as well as some fragmentary material considered to belong to Teleocrater. These bones include a maxilla (tooth-bearing bone of the middle of the snout), frontal (part of the skull roof above the eyes), and a quadrate (part of the cranium's jaw joint). Although these fragments make it difficult to reconstruct the skull of aphanosaurs, they do show several notable features. For example, the shape of the maxilla shows that aphanosaurs had an antorbital fenestra, a large hole on the snout just in front of the eyes. Coupled with an antorbital depression (a collapsed area of bone which surrounded the fenestra), these indicate that aphanosaurs belonged to the group Archosauria. A partially-erupted tooth was also preserved on the lower edge of the maxilla. This tooth was flattened from the sides, slightly curved backwards, and serrated along its front edge. These tooth features indicate that aphanosaurs were carnivorous, as many meat-eating reptiles (including theropod dinosaurs such as Velociraptor) had the same features. The front edge of the maxilla also has a small pit, similar to some silesaurids. The rear part of the frontal possessed a round, shallow pit known as a supratemporal fossa. In the past it was believed that only dinosaurs possessed supratemporal fossae, but its presence in aphanosaurs (and Asilisaurus, a silesaurid) shows that it was variable among many avemetatarsalians. As a whole, known aphanosaurian skull material possessed no unique features, meaning that the rest of the skeleton would have to be used to characterize the group.
Aphanosaurs have many distinguishing features of their cervicals (neck vertebrae). The cervicals are very long compared to those of other early avemetatarsalians. As with most other reptiles, the vertebrae are composed of a roughly cylindrical main body (centrum) and a plate-like neural spine jutting out of the top. In the anterior cervicals (vertebrae at the front of the neck), a pair of low ridges run down the underside of the centrum. These ridges are separated by a wide area with other shallower ridges, making the centrum roughly rectangular in cross-section. The neural spines of the cervicals are also unique in aphanosaurs. They are hatchet shaped, with front edges that taper to a point and drastically overhang the centrum, at least in the front and middle parts of the neck. The upper edge of the neural spine is thin and blade-like, but the area immediately below the edge acquires a rough texture and forms a low, rounded ridge. These features are all unique to aphanosaurs.
As in other reptiles, aphanosaurian vertebrae also have small structures which articulate with either other vertebrae or the ribs which connect to each vertebra. The structures which connect to vertebrae in front of them are called prezygapophyses, while those that connect to vertebrae behind them are called postzygapophyses. The structures which connect to the ribs also have different names. In most archosaurs, the heads of the ribs are two-pronged. As a result, there are two areas on the side of each vertebra for connecting to a rib: the diapophysis in the upper part of the centrum and the parapophysis in a lower position. However, some cervical ribs are very unusual in aphanosaurs due to possessing a three-pronged head, although this feature only occurs in ribs at the base of the neck. In conjunction with this feature, the vertebrae in that area have a facet for the third prong just above the parapophysis, which has sometimes been classified as a 'divided parapophysis'. The only other archosaurs with this feature were the poposauroids, which explains how Yarasuchus had been mistaken for a poposauroid in the past.
In addition to these features which are unique among avemetatarsalians, aphanosaurs also have a few more traits present in other groups. In vertebrae at the front and middle of the neck, the postzygapophyses have additional small prongs just above the articulating plates. These additional prongs are termed epipophyses, and are common in dinosaurs but likely independently evolved due to being absent in other groups of avemetatarsalians. The body vertebrae have a different type of secondary structure. A small structure (hyposphene) below the postzygapophyses fits into a lip (hypantrum) between the prezygapophyses of the following vertebra, forming additional articulations to assist the zygapophyses. These hyposphene-hypantrum articulations are present in saurischian dinosaurs as well as raisuchids, and are often considered to help make the spine more rigid.