The formal complaint accuses Formula One, which is run by controversial sports mogul Bernie Ecclestone, of unlawfully dividing revenues.
"The EU has received the complaint and will evaluate it," said European Commission spokesman Ricardo Cardoso in an email, without adding any further details.
The two teams also confirmed the complaint.
"Sahara Force India is one of two teams to have registered a complaint with the European Union questioning the governance of Formula One and showing that the system of dividing revenues and determining how Formula One's rules are set is both unfair and unlawful," the team said in a statement.
Formula One is firmly controlled by Ecclestone and a small coterie of top teams that includes Mercedes, Ferrari, McLaren, Red Bull and Williams.
Smaller teams have long threatened to take their grievance to the EU in an effort to reorganise the sport's revenue sharing, which remains secret.