France top the group with six points while Ecuador and Switzerland each have three. Honduras have now lost twice and are facing likely elimination.
Honduras did at least have the satisfaction of scoring their first goal at a World Cup finals since 1982 when striker Carlo Costly drove home after 31 minutes to put them 1-0 up.
Their advantage was short lived because Valencia levelled the score only three minutes later. The striker slid in at the far post after a shot from defender Juan Carlos Paredes was deflected across the face of goal.
Honduras thought they had taken the lead again on the stroke of halftime. Costly headed against the bar and his fellow striker Jerry Bengtson bundled the rebound over the line but his effort was ruled out for handball by Australian referee Benjamin Williams.
Valencia, no relation of Ecuador's captain Antonio Valencia, grabbed his second goal of an entertaining game with a downward header from a freekick after 65 minutes.
He was also on target in Ecuador's 2-1 defeat by Switzerland in their opening game.
Ecuador, who reached the last 16 in 2006, face the rampant French in their last group game while Switzerland meet Honduras. France beat Switzerland 5-2 earlier on Friday.
Honduras, at their third finals, have yet to win a World Cup game.
