Wigan stole in front through a penalty from Shaun Maloney after 30 minutes following a foul from Martin Skrtel on Victor Moses.
While Luis Suarez struck just two minutes into the second half, and had a second effort disallowed for handball, Wigan responded and claimed a winner from the unlikely figure of Gary Caldwell as Liverpool suffered a fifth league defeat in six games, and a second in four days following a 3-2 loss at QPR.
Kenny Dalglish's side, who stand seventh, are now only two points clear of Sunderland and are five adrift of Newcastle, who have played a game less. Wigan remain in the bottom three but have drawn level with QPR and are within a point of safety.
Soaked in dazzling sunlight on a wonderful spring afternoon, the two sides started slowly as they laboured their way through the early stages with squinted eyes and arms over their foreheads.
A Steven Gerrard free-kick was almost headed into a dangerous area at the far post by Skrtel but for a crucial block by Emmerson Boyce on eight minutes.
Suarez neatly set Stewart Downing free to lash a half-volley wide of the far post halfway through the first half - then, despite having the lion’s share of the few chances created as well as a stronghold on possession, a minute later Liverpool conceded a penalty when Skrtel’s high foot clattered Moses.
It was five further minutes before the spot-kick was taken thanks to the extended treatment which would eventually lead to Moses being replaced by Albert Crusat, but Maloney held his nerve with his low effort from 12 yards virtually unstoppable.
As had been the case when the two sides met at the DW Stadium in December, Wigan goalkeeper Ali Al Habsi frustrated the Reds on a number of occasions.
Suarez’s curling drive from 25 yards on 40 minutes was met by a superb double-handed parry, while Gerrard’s shot from a tight angle on the left in stoppage time was tipped over the bar by a reflex save after taking a wicked deflection.
Liverpool emerged strongly after the break and levelled inside two minutes. Gerrard was the provider with a cute cut-back to Suarez and the Uruguayan caressed the ball across goal and inside the far corner with a lovely first-time finish.
Just seven minutes later, Suarez had the ball in the net again. However, he clearly punched the ball home after Skrtel's header had hit the woodwork and was booked to cut short his celebrations.
Wigan threatened in bursts but their winning goal was still rather unexpected. A free-kick was only half-cleared by Liverpool and when the ball deflected into the path of Caldwell, he showed the composure of a seasoned forward to take a touch past his man and slot the ball through the legs of Reina.
Finishing chances off has been Liverpool's problem all season and they continued to be wasteful at Anfield, so much so that Dalglish resorted to handing a debut to young forward Raheem Sterling when he replaced Dirk Kuyt late on.
However, despite Suarez firing straight at Al Habsi following a flick-on from Andy Carroll, Liverpool were unable to find a way through the away defence as they lost once again.