The relegation-threatened Latics looked on course for three much-needed Barclays Premier League points as they clung onto a 21st-minute lead given to them by an excellent Charles N'Zogbia strike at the DW Stadium.
However, after Ali Al Habsi had saved one Mikel Arteta spot-kick, Wigan's luck ran out as Baines struck from 12 yards on 77 minutes after a Hugo Rodallega handball.
Wigan were the more adventurous side early on and fully deserved to go ahead. Their breakthrough came after James McCarthy picked out N'Zogbia in the area with a delicate chip over the defence. The Frenchman's control initially let him down and he then stumbled as Howard challenged, but he recovered quickly and turned to curl the ball home from a tight angle.
The visitors were handed a glorious chance to equalise in the 35th minute when N'Zogbia was caught out by a short Baines free-kick and tripped Osman in the corner of the area. Despite Baines having scored the Toffees' last two penalties, Arteta took responsibility and he was denied as Al Habsi saved superbly to his left.
N'Zogbia was forced off early in the second half with a hamstring injury after 53 minutes and was replaced by Victor Moses, who brought two good saves out of Howard within minutes of coming on. But Wigan were punished for another error as Rodallega needlessly handled at a corner and referee Lee Mason pointed to the spot again, and this time Baines ensured there was no let-off as he blasted the ball into the roof of the net.
Source: PA
Source: PA