I'm a Brazilian citizen currently living in Czech Republic, in Pilsen.
If I take a bus to visit Romania for 90 days and enter the country by road will I have to go through an immigration office to cross the border?
You should go through at least two, potentially colocated checks (an exit check in Hungary and an entry check in Romania). You might undergo additional checks if you transit through Serbia or Ukraine or if you encounter some random Czech, Slovak, or Austrian check.
Yes. Romania is not yet a Schengen member, so the border with Hungary is indeed supervised.