The Latics were handed a second straight defeat to lie bottom of the table, whilst Chelsea retain their position on top with six points.
Mike Pollitt had to make a late replacement to Wigan's number one Chris Kirkland in goal, following the latter's injury in the pre-match warm-up.
However, the veteran Pollitt was beaten after only four minutes with an exquisite free kick from Deco, who scored his second goal in two games for Chelsea.
Zaki had a chance to equalize four minutes later, but his low shot was cleverly blocked by Petr Cech.
Cech parried another Zaki effort in the 26th minute, as the Egypt striker proved to be Wigan's main source of danger during the first half.
Daniel de Didder came in for Jason Koumas at half-time, as Steve Bruce was hoping to avoid his team's second successive defeat.
But the second half did not witness much action until the introduction of Olivier Kapo late in the game.
The Frenchman almost leveled the scoring with a powerful right-footed shot, but the watchful Cech produced a superb save to deny him.