The three-aisled basilica located southeast of the theater is 38.20 m long and 16.15 m wide. It consists of a semicircular apse with a synthronon and three aisles, defined by colonnades and a narthex at the western end. At the eastern end of the south aisle, a single-aisle church was built in the 13th century, utilizing sections of walls and materials from an earlier structure.

 The narthex connects to the main church through three openings leading to the respective aisles. The central aisle featured a tribe, a three-part entrance flanked by two columns topped by an arch. A side door on the north wall of the narthex provides access to a complex of annexes, where the baptistery was likely located. The central nave is paved with limestone slabs originating from buildings of the Roman and Hellenistic periods. At the corners of the triumphal arch that once rose in front of the sanctuary’s apse, two pedestals have been used, each bearing the engraved names of great military figures of antiquity, Aristomenes and Alexander, respectively. Evidently, their selection and placement in this specific location cannot be coincidental.

Three carelessly constructed buttresses, dating from a later period, support the apse of the sanctuary from the outside. The colonnades that supported the aisles consisted of ten unfluted limestone columns with marble Ionic bases that originated from the proscenium of the theater. The marble capitals featured arch motifs.

 The basilica had no gallery above the side aisles; the central aisle was covered by a gabled wooden roof, while lower single-pitched roofs covered the two side aisles. Approximately in the middle of the central aisle, between the fifth and sixth columns of the northern colonnade, the foundations of the pulpit and the staircase leading up to it from the north aisle were discovered. To the east of the central aisle, a platform for the sanctuary was formed, defined by a step and separated from the rest of the church by a low barrier. The stone threshold, small columns, and sections of marble friezes have been preserved. On the paved floor of the raised platform of the sanctuary, one can see indentations from the four legs of the Holy Table, as well as from the four bases of the small columns that supported the ciborium above the Holy Table.

Inscriptions were used as building material, primarily in the floor of the central nave and in the bases of the colonnades, with the inscribed surface visible and exposed to the footsteps of the faithful.