The Williams driver passed Sauber's Felipe Nasr between Turns 5 and 6 during FP2, which had been temporarily halted after Fernando Alonso's McLaren ground to a fiery halt.
The Finn was summoned to see the stewards, who ruled that he had not done enough to avoid the infraction. As a result, Bottas was issued with a three-place grid drop and two penalty points on his licence - his first points of the season.
"The driver of car #77 [Bottas] admitted he overtook car #12 [Nasr] under red flags," a statement from the FIA read.
"The stewards, in applying the penalty, took into consideration that despite the considerable speed difference between the cars, the driver of car #77 could have avoided overtaking under the red flag."
Bottas is not the only driver facing a grid drop in Brazil: Red Bull's Daniel Ricciardo will fall ten places after the team opted to use Renault's upgraded engine.