After conceding twice in the opening ten minutes at West Ham last week, the Latics held out for less than four minutes before the Portugal international fired in a stunning free kick.
But the big spending London side found the going a lot tougher than they did in the 4-0 opening day win over Portsmouth and only a late save from Petr Cech denied the Latics a point.
Wigan suffered a big blow before-kick off when keeper Chris Kirkland was a late withdrawal after a knock in the warm-up and Mike Pollitt took over.
Titus Bramble replaced Paul Scharner (ankle) and Jason Koumas was in the starting line-up with Olivier Kapo on the bench.
Chelsea had Michael Ballack and Michael Essien back and England coach Fabio Cappelllo was among the 18,139 crowd at the JJB Stadium.
He saw Chelsea get a dream start snatching the lead after Lee Cattermole gave away a dubious free-kick for handball five yards outside the box.
Deco took responsibility and made no mistake, beating the wall with a terrific strike which gave Pollitt no chance.
Wigan hit back strongly with Wilson Palacios testing Cech at his near post with a piledriver and the keeper again earning his money by blocking another from Amr Zaki after Koumas played him in with a superb ball.
Maynor Figueroa was inches away with a long-range effort, before Ricardo Carvalho almost got a second for Chelsea with a powerful header just over the bar.
Wigan had a penalty claim turned down when the keeper appeared to push Palacios as a corner came in and Cech then came to the rescue again, keeping out another shot from Zaki as the Latics hunted an equaliser.
Chelsea felt they should have had a penalty when Nicolas Anelka went down with Emmerson Boyce close by. But the replay showed ref Alan Wiley got it right and the visitors had to settle for the 1-0 half-time lead.
Wigan battled away in the second half with Egypt striker Zaki a willing workhorse, but they failed to really test Cech, an imposing figure, in the Chelsea goal.
Steve Bruce threw on an extra striker for the last five minutes with Henri Camara back in the fold after spending all last season on loan at West Ham.
But it was midfielder Kapo who almost made it a fairytale ending for the Latics. He came off the bench to replace Palacios and forced a top-quality save from Cech with a fierce strike from 25 yards.