A stunning strike from the Brazil international earned the victory for the home side who now have a slim lead to defend in the second leg
The match began in equilibrated fashion as neither side controlled the contest but instead relied on the pacy play of their respective forwards to create goalmouth opportunities.
Alvaro Negredo was the first to have a clear chance at goal as the Spain international was found unmarked in the 18-yard box by a Jesus Navas cross from the right. The resulting volley found the wrong side of Diego Alves' post, to the delight of the goalkeeper who looked beaten by the striker's attempt.
Jonas responded in the 18th minute, when a strike from outside the box had the Valencia fans celebrating a goal, but Los Che's faithful were fooled as his shot scraped past the post, hitting the netting in the process.
Then the Mestalla erupted once more, but this time the fans had real reason to celebrate. Picking up the ball on the left side of the box, Jonas easily beat Negredo by quickly transferring the ball from his left foot to his right and in one fluid motion, the striker curled his effort into the right side of Andres Palop's goal.
Ten minutes later, the home side nearly doubled its advantage when Jeremy Mathieu dribbled up the left side and flicked the ball on to Jordi Alba. With a clever back-heel, Alba returned the ball to Mathieu who found his way into the box and shot just past the post.
In the second half, the home side once again threatened to increase the scoreline as both Jonas and Alba were guilty of missing open headers. The Brazilian put his chance over the crossbar while the left-back hit his attempt directly at Palop.
Los Rojiblancos nearly made Valencia pay for their missed opportunities as Jesus Navas dribbled up the right side at will, causing havoc whenever he picked up the ball.
After swerving into the middle, a looping cross from the winger found Manu Del Moral, whose glancing header struck the crossbar. This would be the away side's last opportunity to equalize as Unai Emery's men played out the remainder of the match to earn the victory.
With the win, Valencia will play the second leg in Seville on January 11 with a marginal lead to defend. Having only lost 1-0 away from home, Marcelino's men still have an opportunity to reverse the score and will have to win by two goals if they are to progress to the last eight of the competition they lifted in 2010.