For the second consecutive home game, Wigan were left to count the cost of their inability to convert chances into goals as they dominated proceedings but were unable to find the back of the net.
A superb performance from West Ham's England keeper David James helped keep the home side at bay but it was the lack of finishing power that was eventually to be Wigan's undoing.
Second-half strikes from Hayden Mullins and David Connolly earned West Ham a victory they scarcely deserved, but the visitors certainly showed the home side what finishing is about.
Mullins struck first in the 80th minute, when he picked up a neat pass from substitute Neil Mellor and slid the ball past Wigan keeper John Filan.
Five minutes later Connolly scored a superb individual effort after picking up the ball just inside the Wigan half and jinking through the defence before blasting the ball into the net.
It was cruel on the home side as Nathan Ellington, Lee McCulloch and Jason De Vos had all seen James produce tremendous saves to deny certain goals.
But Ellington also missed a golden chance at the start of the second half and McCulloch and Gary Teale were both guilty of glaring misses.
And indeed Wigan's consolation goal in the dying seconds came from the boot of a Hammers player.
Defender De Vos sent over a low cross that eluded both Ellington and Neil Roberts only for Wayne Quinn to deflect the ball past his own keeper.
It was too little too late and Wigan boss Paul Jewell's venture into the transfer market for more striking power will no doubt gather momentum in the days ahead.