The share price jumped 7.43 percent on the Sao Paulo stock exchange, despite Ibovespa falling 0.28 percent.
It came a day after Bolsonaro announced he wouldn't be using his veto powers to block the merger between two of the world's three biggest aviation companies.
Embraer's shares had taken a nose dive last week after Bolsonaro had expressed concerns over the deal.
But now the $5.2 billion deal, which will see Boeing take control of Embraer's commercial airplane manufacturing business -- 80 percent of its operation -- will go ahead.
Embraer will only retain control of its military division.
On Thursday, Bolsonaro had said he was satisfied that "the final proposal preserves (Brazil's) sovereignty and national interests."
Embraer was founded as a state group in 1969 before being privatized in 1994, although the Brazilian government retained a "golden share" giving it the right to veto strategic decisions for the company.