The Ecuador winger was at his best, particularly in the first half when the Latics dominated the action but only had the one goal from Hugo Rodallega to show for it by the break.
But the Colombian's strike proved to be enough to finish an up-and-down season on a high for the Latics with their first win in eight games.
Valencia was a surprise inclusion but the absentees included Paul Scharner, Chris Kirkland and Mido.
Portsmouth included Wigan target Jermaine Pennant, the player who could replace Valencia next season if Steve Bruce gets his way.
It was Valencia who carved out the first chance with the Pompey defence giving him room to race into the box.
But rather than shoot, he opted to square it for Rodallega but he hammered it well over from eight yards.
A long throw in from Mario Melchiot caused problems for Pompey and the ball ran to Michael Brown but he failed to cash in after hitting a tame shot wide.
But the Latics went agonisingly close when a well struck free-kick from Daniel de Ridder was tipped over the bar by Asmir Begovic.
Valencia threatened again but de Ridder failed to reach the cross and the ball flashed across the face of goal.
A great block by Richard Hughes denied de Ridder a great chance, but Wigan got the goal they had been threatening after 26 minutes.
On form Charles N'Zogbia fired in the cross from the left and Rodallega could hardly believe his luck when the ball landed at his feet for a simple tap in to register his third in four games after a deflection off Sol Campbell.
John Utaka and Hughes combined to give Peter Crouch a sight of goal but his weak shot was easily held by Richard Kingson.
Skipper Melchiot was unlucky not to get a second for the Latics after a neat link-up with Rodallega was thwarted by the keeper.
Valenica was just inches away from cashing in after Pompey waited in vain for an offside flag.
Rodallega hammered one into the side-netting and the lively de Ridder tested the keeper as Wigan hunted the killer goal, but the first-half effort ultimately proved decisive.