Rossi was issued with three penalty points which, allied to one he collected earlier in 2015, means he will start next weekend's Valencia finale from the back of the grid.
Rossi heads Yamaha team-mate Jorge Lorenzo in the standings by seven points but is now seeking to overturn his sanction, having appealed to the Court of Arbitration for Sport.
Full FIM Statement:
"On the basis of Article 3.4.2, para 3 of the FIM Road Racing World Championship Grand Prix Regulations, Mr. Valentino Rossi has filed an Appeal against the decision taken by the Race Direction of the Shell Malaysia Motorcycle Grand Prix in Sepang, penultimate round of the FIM MotoGP Grand Prix World Championship, and confirmed by the FIM Stewards, to award 3 penalty points to Mr. Rossi following an incident on Turn 14.
"In appealing to the Court of Arbitration for Sport (CAS), Mr. Rossi seeks annulment or reduction of the penalty. He further requests stay of execution of the decision in accordance with Article R37 of the Code of Sports-Related Arbitration.
"The FIM will not comment any further at this time."