Autosport had reported that Yamaha were under investigation by stewards for allegedly breaching homologation rules with engines used in the season-opening Spanish Grand Prix.
An FIM ruling said Yamaha failed to respect the protocol due to an "internal oversight" and docked the constructor double the points they earned from Fabio Quartararo's victory in Jerez.
The Monster Energy Yamaha factory team have also had 20 points deducted from their championship tally, while satellite outfit Petronas Yamaha SRT were docked 37 points.
The penalty drops Yamaha to third in the manufacturers' standings on 158 points behind new leaders Ducati (171) and Suzuki (163).
None of Yamaha's riders have been docked points in the riders' championship, with Frenchman Quartararo, Spaniard Maverick Vinales and Italian Franco Morbidelli all within 25 points of Spanish leader Joan Mir of Suzuki. (Reporting by Hardik Vyas in Bengaluru; Editing by Ken Ferris)