The deal, valued at around $4.75 billion (£3.59 billion) will give the aerospace giant control of Embraer’s commercial aircraft business.
It will also significantly boost Boeing’s stake in the smaller aircraft market, better placing it to take on rival Airbus.
Back in April, Airbus entered into its own such agreement with Bombardier, taking control of its C-Series programme.
Boeing will hold an 80% ($3.8 billion / £2.9 billion) stake in the joint venture while Sao Paulo-based Embraer will hold the remaining 20%.
Boeing and Airbus have long held a duopoly over the larger aircraft market, and by taking Embraer and Bombardier, respectively, under their wing, the deals are expected to drive a similar rivalry across the smaller aircraft market.
"The agreement with Boeing will create the most important strategic partnership in the aerospace industry, said Paulo Cesar de Souza e Silva, Embraer chief executive officer and president.
"The business combination with Boeing is expected to create a virtuous cycle for the Brazilian aerospace industry, increasing its sales potential, production, creating jobs and income, investments and exports, and in doing so, adding more value to customers, shareholders and employees."