Ivan Ramis volleyed the hosts into an eighth-minute lead and James McArthur profited from a loose ball two minutes after the break to earn the Latics a first win since their 4-1 League Cup rout of the same opponents a month ago.
Sam Allardyce’s side had made their best start for 13 years but with their muscular approach all-too predictable, the win that would have propelled them fourth never looked likely.
It was typical, Allardyce will no doubt muse, that Ramis – a man he tried to sign in the summer – did the early damage but his own side’s cutting edge was in scant supply and James Tomkins’ late header was a mere consolation.
Wigan had set the early tempo, Arouna Kone a common denominator in West Ham worries but the breakthrough came from an unlikelier source and so sweetly did Ramis meet Jean Beausejour’s corner, there were surely gasps amid the cheers.
The defender might have undone his fine work with a blatant check on Mohamed Diame in a dangerous area but Mark Noble curled harmlessly against the wall.
An Andy Carroll flick gave ex-Newcastle team-mate Kevin Nolan a sniff, while another knockdown afforded James Collins an effort on goal, scuffed though it was.
But the visitors’ best chance to restore parity came from the left flank, Matt Jarvis’s inswinging cross only narrowly evading the right boot of Yossi Benayoun (32).
Wigan had ample further chances of their own, Beausejour and James McCarthy denied from range, but breathing space came and was timely, McArthur drilling home Shaun Maloney’s lay-off two minutes after the restart.
Allardyce called for the fresh legs of Modibo Maiga but the striker’s first touch was a shot dragged horribly wide and when a deep cross dropped into Carroll’s path soon after, the big forward swiped at air.
Carlton Cole and Gary O’Neil entered the fray as Allardyce tinkered again in search of late reward but Nolan saw his shot blocked, Cole his header loop high and shoulders sagged.