The incident occurred when the senior Congress leader was about to sit in his car in Rajapur village after attending a function in Ahmednagar assembly constituency, he said. An activist ran towards him and threw ink on Thorat's clothes.
The attacker - identified as Bhausaheb Hasse - was immediately caught by police as he attempted to escape.
Thorat's supporters ransacked a nearby Shiv Sena office and blocked roads to protest against the incident, an official said.
The revenue minister has appealed to his supporters to maintain calm. This is the second incident of its kind within a fortnight in Maharashtra where a senior politician was targeted.
On Aug 8, Cooperatives Minister Harshwardhan Patil was attacked by some tribal activists who threw some liquid on his face which injured his eye.
Both Thorat and Patil have demanded a probe into the incident.