This is complete inaccurate.
The truth of the matter is that Bolsonaro is still president, but he has burned so many bridges, that he is virtually isolated, alone and powerless.
The executive is effectively being run by his three top ministers (all civilians) - Guedes the minister of economy, Moro the minister of Justice and Mandetta the minister of Health. They are literally ignoring Bolsonaro and they have the full support of both houses of congress, the supreme court and the vice president (General Mourao). Bolsonaro will not fire them because if he does, he is very likely to be impeached.
The fact that the top ministers of the executive, Congress, the Judiciary, the state governors and local Mayors are keeping the country afloat, taking proper measures and curtailing Bolsonaro's actions is an example of the Democratic system and Brazilian institutions working as they should.
A truly functional democracy does not and cannot have a single critical point of failure in its elected president.