This species is characterized by its thin-textured ovate leaves with quite short petioles, slender flexuous inflorescences, calyx lobes that are markedly unequal in size, short white corollas, and rather small white fruits. The four calyx lobes are generally 1-2.5 mm long with one of them about twice as long as the others. The corolla tubes are 2.5-3 mm long.

Gonzalagunia ovatifolia similar to and had been confused with Gonzalagunia rudis. These were separated by Taylor (in Lorence et al. 2012) by their calyx lobes, obtuse to rounded and glabrescent in Gonzalagunia ovatifolia vs. acute and densely pubescent in Gonzalagunia rudis, and wider larger leaf blades (4.6-17 x 2-8 cm) in Gonzalagunia ovatifolia vs. narrower smaller leaves (3-11 x 1.5-5 cm) in Gonzalagunia rudis. Gonzalagunia ovatifolia is also similar to Gonzalagunia sessilifolia of western South America, and their separation probably deserves further study.