Valencia continued his fine form for his country as he scored for the sixth straight international game to see Reinaldo Rueda's men to an important win in Group E.
Carlo Costly had put Honduras ahead before Valencia's equaliser in the first half and his second in the 65th minute proved to be the winner at the Arena de Baixada in Curitiba.
Ecuador, who suffered a late loss to Switzerland in their opening game, saw just one change to their starting XI as Oswaldo Minda took Carlos Armando Gruezo Arboleda's place in midfield.
Frickson Erazo's long pass put Valencia through the centre of the Honduras defence, but the Pachuca forward missed the target in a one-on-one with Noel Valladares.
Ecuador looked most dangerous on the counter-attack, while Suarez's men had a good chance in the 27th minute.
Valencia was quickest to react to Juan Carlos Paredes' deflected shot from the right to tap in the equaliser at the back post.
Referee Ben Williams correctly ruled the goal out for a handball – while Bengtson also appeared to be offside – in a dramatic finish to the first half.
Dominguez kept out Beckeles' 20-yard effort early in the second half, while Ecuador were unlucky not to be awarded a penalty in the 58th minute when Felipe Caicedo appeared to be brought down.
Bengtson forced Dominguez into a save down low to his left moments later before Valencia put Rueda's side ahead in the 65th minute.
The 24-year-old climbed highest to nod in Walter Ayovi's fizzing set-piece from the left and the South Americans held on late in the encounter for a key win.
