Promotion-chasing Wigan took their unbeaten run to 17 games but had to ride their luck at the seaside.
TV cameras showed that Blackpool, who dominated much of the game, should have been awarded a goal midway through the second half when a Paul Dalglish header which was scooped back from over the line by impressive keeper John Filan.
Blackpool could have gone ahead inside the first minute when Dalglish, cooly relishing taking on his former club, headed a close range effort straight at Filan.
A Keith Southern shot was deflected just wide and another superb long range effort by Dalglish forced Filan to save at full-stretch before the Latics took the lead after 12 minutes.
The goal came through sloppy Blackpool defending when Chris Clarke and Simon Grayson failed to clear a loose ball on the edge of the area as Tony Dinning arrived late in the box to hit a powerful 12-yard shot past Phil Barnes.
The pattern of Blackpool domination was not interrupted for long, with Dalglish forcing another save from Filan after being put clean through as Wigan tried to play the off-side trap and a Keith Southern shot rebounded off the post.
The second half was a tighter affair but on 65 minutes a John Hills corner found Dalglish and his flick header seemed to have beaten Filan, and John Murphy's following up shot certainly crossed the line, but substitute referee Mike Ryan made himself extremely unpopular with the home fans by denying the goal.
Wigan again hit Blackpool with a sucker punch in the 86th minute when hardworking substitute Michael Flynn chased down a long throughball which Barnes had come out of his penalty area to clear. The big keeper hit his clearance straight at Flynn who had no problem latching onto the rebound to seal a victory, marred by pitch invasions from both sets of fans.
Dalglish said afterwards: “I knew it was a goal and the TV replays have proved it, I was jumping round like a lunatic but the ref took no notice.†But Wigan boss Paul Jewell said: 'We did not play well at all today but we have gone 17 games unbeaten so we must be doing something right.â€