The Latics defender powered in from a corner with four minutes remaining as the visitors completed their remarkable survival act and hammered the final nail in Rovers' miserable season.
Blackburn supporters, perhaps already resigned to their fate, had turned the game into one long protest against manager Steve Kean and owners Venky's and several invaded the pitch at the final whistle.
A live chicken had even been released early in the game, presumably in protest against Indian poultry giants Venky's, whose takeover in 2010 is pinpointed by many as the start of the club's demise.
The hen, draped in Rovers colours, walked around Ali Al Habsi's goal area before it was caught by the Wigan goalkeeper and Blackburn striker Ayegbeni Yakubu and carried away by a steward.
By then there had already been several anti-Kean or Venky's chants from the supporters.
With banners as well, the Rovers fans were preoccupied with the state of their club with the action clearly of secondary importance.
On a worrying note, Gael Givet, who has a heart condition, left the action at half-time amid rumours of further problems but he was seen soon after taking a seat in the stand.
What action there was saw Wigan do the early attacking with Franco di Santo bursting clear only to shoot straight at Paul Robinson.
Di Santo then fired over with another effort after a good knockdown by Jean Beausejour.
For Blackburn, Junior Hoilett blasted over and then briefly excited with a mazy run before shooting tamely at Al Habsi.
David Dunn failed to trouble the keeper with an optimistic long-range effort before James McCarthy sparked a good Wigan counter-attack which ended when Robinson claimed Emmerson Boyce's cross.
Victor Moses almost punished Scott Dann as he pinched the ball on the touchline and skipped into the box but Robinson was equal to his effort.
A free-kick from Shaun Maloney caused more problems in the Blackburn box as Anthony Modeste failed to clear but Gary Caldwell shot wide.
Rovers briefly sparked into life as Yakubu broke from deep but he was crudely barged over by James McArthur, who was lucky not to be booked.
When Morten Gamst Pedersen smashed a free-kick from wide on the right straight through the box it seemed Rovers fans were ready to give up.
"That's why we're going down," they sang, in reply to a chant from Wigan fans suggesting similar.
Dunn, a lifelong Rovers fan, seemed dejected as he was forced off the field just before half-time, perhaps after suffering a further recurrence of his Achilles problem.
As the second half began, a Rovers fan ran across the pitch waving his season ticket in the air.
It was a curious protest because when he reached the dugout he showed it to Wigan boss Roberto Martinez, rather than anyone connected to his own club.
As the game proceeded, Rovers began to play some of their best football of the game in spite of their dreadful predicament.
Dann headed down a Pedersen corner and Yakubu acrobatically got a shot on target but it was blocked on the line and Wigan scrambled clear.
The hosts were then unlucky not to be awarded a penalty after Boyce appeared to kick Hoilett's standing leg as he shaped to shoot.
There were appeals from the players but not so many from the fans, who were soon back chanting about Venky's.
Modeste then shot at Al Habsi before Wigan had their own penalty appeal turned down when Moses went down in the area.
Martin Olsson weaved his way into the Wigan box but Al Habsi gathered his cross-shot well.
Wigan then rallied to produce a strong finish and snatch their priceless victory.
Robinson did brilliantly to keep out a fierce shot from Moses and McCarthy's follow-up attempt before Maloney headed a golden chance over.
The winner came from a corner as time ran out.
Alcaraz timed his leap superbly to meet Beausejour's deep cross and powered a header goalwards which Robinson, despite a valiant effort, could not palm out.
The Wigan players all ran to the Paraguay international while their large 3,500 following celebrated jubilantly.
Rovers fans, by contrast, continued their protests with some throwing off their shirts and others invading the pitch at the final whistle.