The three teams were battling to secure 16th place as the curtains were closed on the campaign and Palmeiras ' 1-1 draw at home to Atletico PR was enough to ensure they avoided relegation.
That situation did not look a formality at the Allianz Parque when Potiguar put the visitors ahead in the 10th minute.
Bahia's hopes were extinguished as they let a two-goal lead slip in a 3-2 loss at Coritiba.
When Dudu equalised five minutes from the end Bahia's hopes were all but over and Keirrison added further salt to the wounds with a winning goal deep into injury time.
Vitoria were also sunk by a late goal in their 1-0 defeat at home to Santos.
With the game seemingly heading for stalemate - which would not have been enough to save Vitoria - Thiago Ribeiro scored in the fourth minute of injury time to consign the hosts to their fate.
Elsewhere, champions Cruzeiro rounded off their campaign with a 2-1 victory over Fluminense, as Nilton and Marcelo Moreno goals cancelled out Fred's opener, while second-placed Atletico Mineiro drew 0-0 at already-relegated Botafogo.
Pablo's 50th minute opener put the hosts ahead at the Estadio Orlando Scarpelli, but Rafael Moura levelled with three minutes left on the clock before Wellington Silva grabbed a dramatic winner in the fifth minute of injury time.
That meant that Corinthians were forced to settle for fourth and a place in the qualifying rounds for the Copa despite their 2-1 win over rock-bottom Criciuma.
