Victory saw Chelsea, who could qualify for the Champions League as of right by winning this season's edition (they face champions Barcelona in the semi-finals) move above Newcastle and left them just two points behind fourth-placed Arsenal.
Only the top three teams in the Premier League are guaranteed places in the Champions League proper, with the fourth-placed side set for a qualifying round.
Chelsea's Branislav Ivanovic volleyed home in the 62nd minute to break the deadlock and the goal stood despite furious Wigan protests that he was offside.
Barely a minute later the Serbian defender then preserved Chelsea's lead with a goal-line clearance.
But Wigan, who remained in the bottom three, equalised when Mohamed Diame struck eight minutes from time.
However, Chelsea grabbed a winner late in the match when, after Fernando Torres's volley hit the post, the ball struck Mata on the chest and trickled in.
Furious Wigan manager Roberto Martinez said: "The linesman had a disgusting performance. Today, my players were robbed and they now have a disgusting feeling they don't deserve.
"If you are good at your job then you don't get these decisions wrong."
Interim Chelsea manager Roberto di Matteo sympathised with Martinez, saying: "I think they (Wigan) were unlucky.
"But the result shows we have great spirit. The result keeps us alive and puts the pressure on those who are above us."
League Cup winners and FA Cup semi-finalists Liverpool saw a run of three straight league defeats end with a 1-1 draw at home to Aston Villa.
Brazilian keeper Alexander Doni, making his Liverpool debut in the absence of the suspended Pepe Reina, flapped at a 10th minute cross from former Reds defender Stephen Warnock and Chris Herd turned in the loose ball.
But Luis Suarez, who'd seen a header hit the post, equalised eight minutes from time when he nodded in from close range.
Earlier, Tottenham Hotspur moved into third place, a point in front of north London rivals Arsenal, after a goalless draw at Sunderland.
The closest either side came to a goal was in the 73rd minute when Spurs midfielder Rafael van der Vaart had a shot cleared off the line.
But the Gunners can regain third place against Manchester City on Sunday.
Frustrated Tottenham captain Scott Parker told Sky Sports: "Sunderland set up to get men behind the ball.
"We were a bit surprised at how they set up," the England midfielder said. "We expected them to come at us a bit more but we will take a draw and move on."
West Brom ensured Blackburn Rovers remained in the bottom three with a 3-0 win at the Hawthorns.
Martin Olsson's own-goal gave the Baggies, managed by former Blackburn boss Roy Hodgson, a seventh-minute lead before Marc-Antoine Fortune's 69th minute close-range shot made the game safe.
Liam Ridgewell added a third five minutes from time.
Mid-table Fulham left Bolton looking over their shoulders at the drop zone with a 3-0 win that featured two goals from Clint Dempsey.
United States midfielder Dempsey gave the Londoners the lead with a brilliant 25-yard free-kick in the 30th minute before heading in Damien Duff's cross on the stroke of half-time.
Mahamadou Diarra's first goal for Fulham, 10 minutes from time, put the result beyond doubt.
Elsewhere Everton and Norwich shared the spoils in a 2-2 draw.
Croatia striker Nikica Jelavic scored twice for Everton either side of Jonny Howson's goal before Norwich striker Grant Holt rescued a point for the hosts at Carrow Road after turning in Aaron Wilbraham's pass.
Wolves, still six points adrift at the foot of the table, travel to Stoke in Saturday's late kick-off.
Sunday could witness a decisive stage of the Premier League title race, with second-placed City in danger of falling eight points behind leaders Manchester United if they lose at Arsenal and the champions beat QPR.
Source: AFP
Source: AFP