The golden share allows the South American country to exercise veto power over changes in controlling interest and other strategic decisions at Embraer.
A government official told Reuters Boeings proposal was declined due to its plan to take control of the Brazil-based aerospace company.
An individual familiar with the negotiations said the possible combination could be worth approximately $5 billion to $6 billion.
Brazils air force considers Embraer a strategic company that is fundamental for our national sovereignty, so a possible partnership with Boeing should also be studied from this point of view, the service said in an emailed statement.
The companies first announced in December that they were in discussions about a possible tie-up.