Body compressed, moderately elongate. Mouth terminal. Overall coloration silvery-tan, with silvery highlights on scales, major portion of iris, infraorbitals, preopercle, and opercle. Dorsal portion of iris, together with lateroventral half of head, with the exception of third infraorbital, and ventral portion of preopercle and opercle tinged with yellow. Scales around humeral spot and on lateroventral region of body anterior to anal fin origin also yellowish. Humeral spot visible, although not so conspicuous as in preserved specimens. Concentration of dark chromatophores visible over caudal peduncle, although not forming conspicuous blotch. Dorsal, anal, caudal, and adipose fins reddish-orange. Pectorals yellowish and pelvic fins hyaline.

Astyanax jacobinae can be distinguished from most of its congeners and from all other Astyanax species known from northeastern Brazilian drainages (A. brevirhinus, A. fasciatus, A. intermedius, A. lacustris, A. pelecus, A. rivularis, A. taeniatus) by the presence of a vertically elongated humeral blotch (vs. distinctly horizontally elongated humeral blotch in A. lacustris and A. pelecus), absence of a conspicuous dark stripe from humeral region to caudal peduncle (vs. well defined dark midlateral stripe along most of body length in A. intermedius, A. pelecus, A rivularis, A. taeniatus), three or four outer premaxillary teeth, three maxillary teeth, and 21–26 anal fin rays (vs. five outer premaxillary teeth, one or two maxillary teeth, and 28 anal-fin rays in A. brevirhinus). The new species differs from the majority of Astyanax species by its larger eye diameter (36.8–40.3% vs. 24.7–35.4%, with the exception of A. intermedius among northeastern species that approaches the eye diameter of A. jacobinae with 29.0–36.4%). It can be distinguished from A. turmalinensis by its higher number of maxillary teeth and by the presence of only one humeral blotch (3 or 4 teeth vs. 1 or 2 and presence of two humeral blotches). It can be also distinguished from A. epiagos by having higher number of branched anal-fin rays (19–22 vs. 13–17), three maxillary teeth (vs. 0–2), longer anal-fin base length (27.6–30.7% vs. 18.1–23.2%), shorter distance from eye to dorsal-fin origin (36.0–39.2% vs. 39.5–43.2%), and also by the absence of broad space between infraorbitals and preopercle.