Nemani Nadolo was mistakenly included in the 27-22 defeat at Headingley alongside Hoani Tui and Ignacio Mieres on 3 April.
The decision was announced at a Rugby Football Union disciplinary hearing.
Despite the deduction, Exeter stay ninth in the Premiership where they now have 39 points.
Fijian-born Nadolo, 23, registered for the Devon club on an Australian passport when he joined from Bourgoin in January.
Under the RFU's rules, Premiership clubs' match-day squads can only have two players from outside of Europe, Africa, the Caribbean and the Pacific Islands - a limit they exceeded with the inclusion of Nadolo alongside Tui (New Zealand) and Mieres (Argentina).
