Ecuador suffered a last-gasp defeat to Switzerland last time out, and things appeared to be heading further south when Carlo Costly opened the scoring for Los Catrachos in the 31st minute of Friday's affair.
But Valencia put the team on his shoulders, scoring two more goals in the tournament to keep the South American nation in the hunt for a berth in the knockout round.
France, which smashed Switzerland in a 5-2 victory earlier on Friday, leads the group with six points. Switzerland and Ecuador are level on three points apiece while Honduras bottoms the group with zero points.
Honduras started brightly on Friday and took the lead at the half-hour mark when Costly collected a long ball that was misjudged by the Ecuadorian defense and lashed a half-volley past Alexander Dominguez at the near post.
The goal, which snapped a 510-minute goalless drought for Honduras, was the nation's first in World Cup play since 1982.
The lead, however, was short-lived as Ecuador responded within three minutes. A ball thrown into the mixer somehow managed to squirt to the back post, and while Valencia and Honduras goalkeeper Noel Valladares knew little of the delivery, the Ecuadorian striker was first to react, turning in the shot from close range.
Ecuador completed the comeback in the 65th minute, and it was Valencia again doing the honors.
The goal came in the same manner of the opener against Switzerland as the Pachuca striker got on the end of Walter Ayovi's cross and nodded the delivery into the back of the net, making Valencia the first Ecuadorian player to score two goals in a World Cup game.
It proved to be enough for La Tri as Reinaldo Rueda's men collected the vital victory, leaving them with all to do in their Group E finale against France on Wednesday.
Honduras, meanwhile, will look to regroup ahead of its final group match against Switzerland at the Arena Amazonia, also on Wednesday.