After picking up just one point in their previous three matches, Oswaldo de Oliveira's men were desperate to keep their hopes alive of qualifying for the continental tournament - especially as opponents Atletico PR are one of their prime rivals for a top-four finish.
And Botafogo delivered the goods at their Estadio Jornalista Mario Filho home in Rio de Janeiro, with Elias and Clarence Seedorf goals in the first half complemented with a brace to Bruno Mendes late on to wrap up a crucial three points.
Botafogo now sit in fifth, one point behind Atletico PR (fourth) - who occupy the Copa Libertadores qualifying spot.
In the remaining live automatic places sit Gremio and Goias, with both sides earning home successes on Sunday.
Goias had a 3-1 victory over Internacional - benefitting from the dismissal of the visitors' Rafael Moura in the 67th minute to score late via Hugo and Roni.
Gremio dramatically snatched all three points against Flamengo, earning a 2-1 win as Maximiliano Rodriguez completed his brace in the 88th minute.
With Cruzeiro having wrapped up the title already, Gremio sit second on 60 points in the race for the continental honours while Goias are one back on 59 with three matches to play.
Atletico PR are on 58 points, while Botafogo have 57 - with Vitoria and Atletico Mineiro still mathematical chances of finishing in the top four.
Vitoria, sixth on 54 points, had a 2-0 home triumph over Santos, while Atletico Mineiro fell to 2-0 road loss to Portuguesa to remain on 52 points in seventh.
Mineiro's hopes are all but dashed with a tough run-in too as they are still to face Goias and Vitoria.
Fluminense continued their late resurgence, chalking up consecutive wins with a 2-1 home triumph over Sao Paulo to take them to 15th spot and one point clear of the drop zone.
Bahia also leaped out of the bottom four with a 1-0 road win over relegated Nautico, dumping Coritiba into the zone as the latter were beaten 2-1 at home to Criciuma.
Criciuma won their third match in succession to go 14th, level on 42 points with Fluminense and Bahia.
Champions Cruzeiro were denied a 24th win of the season by the 19th-placed Ponte Preta, with the latter scoring at the death via Leonardo to earn a 2-2 draw.
Ponte Preta remain seven points from safety with three matches to play.
Corinthians and Vasco da Gama played out the matchday's only scoreless draw, with Vasco earning a road point to better their survival chances as they sit in 18th spot - four points from safety.
