An exemplary surgical instrument tracking system includes at least one physical computing device that determines, based on endoscopic imagery of a surgical area and using a trained neural network, an observation for an object of interest depicted in the endoscopic imagery, associates, based on a probabilistic framework and kinematics of a robotically-manipulated surgical instrument located at the surgical area, the observation for the object of interest to the robotically-manipulated surgical instrument, and determines a physical position of the robotically-manipulated surgical instrument at the surgical area based on the kinematics of the robotically-manipulated surgical instrument and the observation associated with the robotically-manipulated surgical instrument.