The edifice was built in the late 15th century, perhaps with the participation of Bartolomeo Bon. The palace consisted originally of two separated sectors, one for each branch of the family, which were later joined by a façade; these are the Ca' Giustinian dei Vescovi (now housing part of the Ca' Foscari University) and the Ca' Giustinian dalle Zogie (now privately owned). Behind the façade, they are separated by an alley which, through a sottoportego, or portico-tunnel, connects to the central portal.
The two sub-palaces share numerous decorative features with the annexed Ca' Foscari. They have an L-shaped plan with four floors, the upper ones having mullioned windows. At the piano nobile they form a six-arches arcade with an interwoven motif of multi-lobes circles. The single windows are ogival, or decorated with a three-lobe motif. Ca' Giustinian dei Vescovi has in the rear a court with a Gothic staircase, while Ca' Giustinian delle Zogie has a large garden.