Several dozen supporters shouted abuse and threw eggs at the team bus, according to local news reports.
The team's best-known player, Dutch midfielder Clarence Seedorf, was among those targeted as the players were returning from Rio Grande do Sul after losing 2-1 to Internacional on Sunday.
Botafogo are fourth in the Brazilian championship standings, equal on points with fifth-placed Goias, to whom they lost 1-0 a week ago.
The top four teams qualify for next year's Libertadores Cup and fans have warned there would be trouble if the club did not secure a place in South America´s top club competition.
After challenging for top spot for much of the season Botafogo have fallen away, taking just four points from their last five matches.
(Reporting by Andrew Downie; Editing by Rex Gowar)
