John Terry's second-half diving header consigned Wigan to a fourth straight Premiership defeat and extended Chelsea's lead to 12 points.
Wigan held firm for 67 minutes before Terry converted Frank Lampard's corner.
Mike Pollitt had earlier saved from Joe Cole, Frank Lampard and Didier Drogba, while Leighton Baines cleared a Hernan Crespo header off the line.
Lee McCulloch was lucky not to concede a first-half penalty after crudely hauling Terry to the ground.
Terry's goal was his second in as many weeks after opening his account for the season in last Saturday's 1-0 home win over Middlesbrough.
But it far from vintage Chelsea, who started with Carlo Cudicini making a rare appearance in goal and Crespo returning from injury.
Although Paul Jewell's Wigan created few openings of their own, they at least proved to be obstinate opponents as they looked to halt their recent slump in form.
Early long-range strikes from Michael Essien and Lampard missed the target, while Pollitt saved from Cole.
A sublime flick from Crespo had played Cole through, but he still had a lot to do before shooting; carrying the ball from inside his own half before cutting inside and striking at goal.
Terry was furious after referee Howard Webb failed to see McCulloch rugby tackle him to the ground as he closed in for a header.
Asier del Horno's sharp thinking then unlocked the Wigan defence.
The defender's quick free-kick was sent goalwards by Crespo and a roar went up around Stamford Bridge, but Baines brilliantly headed off the line.
Pollitt saved from Lampard on the stroke of half-time but the home team were showing signs of frustration against well-drilled, resolute opponents.
Drogba replaced Duff at the break - and the Ivory Coast international would have broken the deadlock within minutes but for Pollitt's block.
Jose Mourinho brought on Eidur Gudjohnsen for Arjen Robben but Wigan maintained their defensive shape, constantly winning offside decisions against Drogba and an increasingly frustrated Crespo.
But Chelsea finally broke through, Pollitt getting a firm hand to Terry's header but not enough to prevent the ball from finding the net.
The Wigan goalkeeper made further saves from Cole and Lampard to prevent Chelsea from extending their lead.
But the Latics never looked like scoring against a team who have not conceded since Darren Fletcher scored against them for Manchester United on 6 November.
Chelsea boss Jose Mourinho:
"This afternoon we deserved to win. We did not play well, but well enough to win.
"They did not have one single chance, we controlled the entire 90 minutes and created some chances."
"In our group we only have one player in a high level of form and that is Joe Cole. It is not good enough in relation to the potential of my team."
Wigan boss Paul Jewell:
"I think that with the exception of one or two chances we kept it quite tight.
"Conceding a goal from a cross and a header was disappointing but I cannot fault my players for effort.
"We are near the end of a difficult period but hopefully after the game against Manchester United it might get a bit easier."
Chelsea: Cudicini, Gallas, Ricardo Carvalho, Terry, Del Horno, Essien, Robben (Gudjohnsen 59), Joe Cole, Lampard, Duff (Drogba 45), Crespo (Geremi 69).
Subs Not Used: Cech, Huth.
Booked: Ricardo Carvalho.
Goals: Terry 67.
Wigan: Pollitt, Chimbonda, Henchoz, Jackson, Baines, Taylor (Teale 79), Skoko, Kavanagh (Bullard 73), McCulloch, Connolly, Roberts (Camara 73).
Subs Not Used: Walsh, Francis.
Ref: H Webb (S Yorkshire).