The result left Venezuela with second place in the group and a last-eight meeting with Group C winners Chile in San Juan. The other quarter-finals pit hosts Argentina against Uruguay while Colombia take on Peru.
Title-holders Brazil, winners of four of the last five tournaments, have already shared a 2-2 draw in the group stage with Paraguay, who qualified as one of the two best third-placed teams along with Peru.
Ecuador bowed out of the tournament with two good goals from Felipe Caicedo in an exciting match that capped a lively final night for the South American tournament's group stage.
Venezuela earlier mounted a remarkable late comeback to snatch a 3-3 draw against Paraguay in Salta.
After a dull opening half-hour, Brazil lit up the match at the Mario Alberto Kempes stadium with a fine headed goal by Pato from Andre Santos's left cross.
Eight minutes later, Brazil might have gone two goals up when Robinho's shot from Maicon's right cross hit goalkeeper Marcelo Elizaga's left-hand post.
Instead, down the other end less than a minute later, big striker Caicedo found space to shoot from the edge of the box and the ball squeezed in under goalkeeper Julio Cesar for the equaliser.
Ecuador could have gone ahead in first half stoppage-time but for the Brazil goalkeeper's diving save from a curling, left-footed shot from the right by Michael Arroyo.
Brazil regained the lead four minutes into the second half when Paulo Henrique Ganso took a ball with his back to goal, turned and slotted it through to Neymar who scored in the top corner.
Caicedo hit his second equaliser just before the hour when Christian Noboa won the ball in midfield and set the striker up to shoot low past Julio Cesar.
Pato put Brazil ahead again within two minutes, netting the rebound after Elizaga parried a shot from Neymar, who then made it four for Brazil in the 72nd by turning in Maicon's low cross.
