Valencia equalised with a far-post poked effort just two minutes later, before heading the winning goal after the break to put his side right back in contention in the group.
Here, Sports Mole takes a closer look at the game to see whether the result was justified.
On target: 9
On target: 5
Was the result fair?
Although Honduras gave a very good account of themselves, Ecuador were the better team with the ball and created the better chances. They had a clinical striker in Valencia to finish the chances, while Honduras resorted mainly to shots from range. It was an entertaining game with no shortage of tough tackles, but in the end it was Ecuador who possessed the greater class and that is what just about shone through in the result.
There were still one or two players a bit eager to throw themselves into a tackle, but their gameplan was more effective overall than against France. A lot of the time they did sit back and play on the break, but as evidenced by the goal that they took the lead with such tactics can cause problems. Overall they just did not have the right kind of player to either hold on to their lead or get back into the game once behind, but they have nothing to be ashamed of.
While Ecuador against Switzerland went in front and were unable to hold their lead, this match showed them in a different light. After going behind they were the more attacking of the two sides and always the more likely to create decent chances. For long spells they held the ball in the Honduras half, and in Valencia they had a striker who took two of the few chances he was presented with. They probably will not go much further if they do qualify from the group, but their attack is certainly capable of causing damage.
Sports Mole's man of the match
Enner Valencia: This one is a no-brainer, really. In a game that was entertaining but lacked something in the way of genuine quality, Valencia stood out with his finishing prowess. His first goal was a real poacher's effort as he ghosted in at the far post to prod home, and his second was a fine header from an excellent Walter Ayovi cross. He was the best player on the pitch, and by quite some distance.
Fortunately for Jorge Guagua his mistake was not costly in the end, but it looked very much to be at the time. He tussled with Honduras striker Carlo Costly from a first-half long ball, but completely lost track of it, which allowed the forward in for the opening goal. His side recovered well, but had they not then the centre-back would have had to shoulder a lot of the blame for a moment of schoolboy defending.
This was a fairly tricky game to officiate for Ben Williams, but he had an excellent match overall. He showed a number of yellow cards, but did not dive into his pocket too early and thus set a precedent. He might have given Ecuador a penalty for what looked to be a foul on Felipe Caicedo by Maynor Figueroa, but the vast majority of calls were spot on.
Honduras: Although not officially out of the World Cup yet, Honduras face Switzerland on Wednesday night with not a lot to play for. Only a big win and the other result going their way will see them qualify.
Ecuador: They have clawed themselves back into contention with this win, and they will need at least a draw and quite possibly a win against France in their next game to beat Switzerland into qualifying for the last 16.