The youngster from Ecuador has attracted a great deal of attention this season and has been linked with a possible move to Manchester United.
It was only Wigan's second away win in 19 games and the emphatic way they accomplished their success is a credit both the team and manager, Steve Bruce.
Goalkeeper Chris Kirkland also took top honours for an outstanding performance as he repeatedly denied an out-of-form Villa side and did much to keep Wigan in contention.
But it was Valencia who took advantage of Villa's frustrating performance which was typical of several displays this season against lowly opposition.
The surprising feature of the goalless first half was Villa's inability to raise their game.
They were fully aware that a win would take them into fifth spot above Everton, but they were continually frustrated by a dogged Wigan defence and in particular goalkeeper Kirkland.
On three occasions he made saves from headers powered in by Zat Knight, Gareth Barry and Gabby Agbonlahor.
Kirkland undoubtedly kept Wigan in the game as Villa became increasingly impatient by their lack of success.
Jason Koumas and Michael Brown dominated the midfield as both Nigel Reo-Coker and Stiliyan Petrov were way below their recent form.
Any hopes of a Villa revival in the second half were quickly dashed by Wigan's opening goal from Valencia after 52 minutes.
The 22 year-old winger, who always displayed the potential to be dangerous, cut in from the right and unleashed a hopeful shot on goal.
The ball took a wicked deflection off the unfortunate Wilfred Bouma and looped over the head of Scott Carson into the far corner of the net.
This was a tremendous set-back for Villa and a massive fillip for Wigan as was subsequently reflected by the Latics' determination not only to retain the lead but to increase their advantage.
Valencia was the player who put the game out of Villa's reach in the 63rd minute.
Emile Heskey, who produced a good work-rate helping out defensively, headed on a ball which Valencia latched on to.
He bore down on Villa's goal and squeezed his close range shot between Carson and the near post.
Villa made a couple of substations but to no avail and skipper Gareth Barry, who was linked with Liverpool a few days ago, was unable to inspire his side to stage a comeback.
When they did threaten danger it was Kirkland who popped up to foil their efforts.
It was a sad ending for defender Olof Mellberg on his final home appearance before linking up with Juventus next season.