The International Automobile Federation said it fined Ferrari $100,000 after race stewards determined the Italian team broke rules against issuing team orders.
Massa had dominated the race until Alonso easily passed him in the 49th lap to take the top position after Massa was told over the team radio that Alonso had the faster car.
Massa's race engineer, Rob Smedley, was heard telling the Brazilian over the team radio, "Fernando is faster than you. Can you confirm you understood that message?"
The finish led to widespread speculation that Ferrari had ordered Massa to surrender the lead. It appeared that Massa made room for Alonso on the decisive turn.
Asked if he had been given instructions to give up the lead, Massa said, "I don't think I need to say anything about that."
Team Ferrari issued a statement denying the allegations, saying it was confident the World Motor Sport Council, which must uphold the decision, would find the charges without merit.
Alonso claimed his second Formula One victory of the year and 22nd of his career, while Massa was aiming the win the German Grand Prix on the one-year anniversary of a near-fatal crash during a qualifying run the Hungarian Grand Prix.
Pole sitter and German crowd favorite Sebastian Vettel finished third, while points leader Lewis Hamilton came in fourth and McLaren teammate Jenson Button claimed the fifth spot.