The Latics scored a last-minute winner through Craig Mahon's smart finish, when it had seemed certain that United would take the points after David Gray had cancelled out Matt Hampson's opener.
On a frustrating evening, United can take positives from the performance of Manucho, as his first competitive start for the Reds was littered with neat touches, clever link-up work and, in one late example, tremendously powerful forward play.
In a brisk opening, both sides struck the woodwork inside the first 15 minutes. Sam Hewson embarked on a neat, slaloming run on the edge of the Latics' area after 10 minutes, but saw his powerful left-footer deflected up onto the crossbar. Five minutes later, Tomasz Cwyka smashed a 30-yarder against the inside of Gary Woods' post.
A see-saw match swung back the other way shortly afterwards when a neat passing move ended with Magnus Eikrem's shot being blocked by goalkeeper Neil Postlethwaite. Young Polish striker Tomasz Kupisz then slammed a snap-shot into the side netting and Woods tipped over a powerful effort from Craig Mahon.
Wigan took the lead shortly after the second half began, as Kupisz sprinted down the left wing and slid back a cross for Hampson to calmly slot into the net.
Manucho came close to a leveller with 20 minutes remaining when he cut inside from the right flank, beat two defenders and hammered a low shot goalwards, only for Postlethwaite to beat the effort away.