Audi confirmed di Grassi was disqualified from the qualification because of a slow break in a tour after his qualifying group. Later he headed the Super Pole session.
Di Grassi was placed under investigation for alleged technical misconduct after his expiry in the second group in the first stage of the qualification.
The rule in question relates to Article 27 (9) of the FE's sports regulations for braking and is only implemented before the race this weekend upon a request from Spark to the FE's supplier.
Now all drivers have to stop at the same level in their tours as they would during a hot lap in group qualifiers.
Motorsport.com understands that excessive lapping of the lap may be related to maintaining the tire pressure before the superpole – but there is no suggestion that di Grassi is doing this at this stage.
The rule is introduced for safety reasons and all teams are informed of the pre-race change.
The FIA Bulletin, which explains the decision, states: "The driver uses more brakes in the inlap during the qualification, then on a flying trip for no reason.
"The time of a superpol must be canceled as a result of the cancellation of qualification times.
"The driver is allowed to start the race at the rear of the net."
Di Grass supercomputers' associate, Stowew Vandouren, lost his time for a superpole not to leave the "prospect for his tour of the superfield, not in the mandatory time window of 30 seconds when the pitlight was red," according to another FIA newsletter.
As a result of the penalties, Sebasien Buemi will start from a pole for Nissan e.dams to Pascal Wehrlein (Mahindra Racing), Daniel Abt, Sam Bird and Vandoorne.
The FIA also announced that the regime for activating the attack regime for the race in Santiago will be the same as in the first two rounds of the Riyadh and Marrakech season.
Drivers are allowed to arm their systems up to five times and must activate the system twice during the race – even after the second lap is completed – for two periods of four minutes.