The defender’s late header ends Blackburn’s 11-year spell in the top flight of English football as the Latics seal their survival.
The visitors largely dominated the match but Blackburn was frustrated not to be awarded a second-half penalty for a foul on Junior Hoilett.
Fans invaded the pitch at the final whistle in further opposition to the club’s management and owners on a night of protest at Ewood Park.
With Rovers knowing that only a win would suffice, Steve Kean made two changes to his side that lost 2-0 at Tottenham. Martin Olsson replaced his brother Marcus at left back, while striker Anthony Modeste came in for Mauro Formica in a more attacking lineup.
Unsurprisingly Wigan was unchanged from its incredible 4-0 win over Newcastle and knew that a point would all but secure its Premier League survival.
It was a frantic start from the hosts as the cries rang out from the Ewood Park faithful venting their anger towards both manager Kean and the club’s owners.
The games first opportunity went to the visitors. David Dunn had possession stolen from him by Shaun Maloney who fed in Victor Moses, but his effort flew well over the bar.
In the strangest of twists the game was paused when a chicken was let loose onto the pitch; a strong visual protest from the Rovers fans to match the chorus of boos.
Wigan continued to press and Paul Robinson produced a smart save to deny Franco Di Santo. Moses provided the assist but Robinson got down to his left and Gael Givet cleared the danger.
However Blackburn responded well and created a chance of its own soon after. Yakubu’s knockdown fell to Anthony Modeste outside the box, but his sliced volley went narrowly over.
With Ben Watson pulling the strings in midfield Wigan continued to dominate the home side which began to sit deeper and deeper. The pace of Moses again had Blackburn reeling, Scott Dann couldn’t stop the winger who coasted into the area but from a tight angle shot straight at Robinson.
The visitor’s frustrations continued. Maloney sent a free kick deep to the far post which Gary Caldwell nodded back across goal. However Watson, in trying to control the ball, took it out of the path of Moses.
Wigan was once again wasteful shortly before halftime when Moses made a mess of his free header, nodding it back to where it came from. Di Santo had whipped in an inch perfect cross that Dann misjudged but Moses couldn’t capitalise.
Blackburn was equally wasteful with its ventures into the Wigan half though. A free kick on the right-hand side was hit hard and wide by Morten Gamst Pedersen and out of reach of the large contingent of his team mates that had crowded the area.
After the break Rovers began the brighter and Pedersen’s rasping shot from the left went just over after a fantastic long ball from substitute Radosav Petrovic.
However Wigan was soon on the front foot, shots from Jean Beausejour and James McCarthy though didn’t trouble Robinson.
Rovers’ best chance came minutes later. Dann towered above his defender to head across to Yakubu but he couldn’t keep his balance and scuffed his shot which was easily blocked.
Another chance fell to Wigan as the second half opened up. Di Santo provided the knock down to Moses but he sent his volley over from 12 yards.
The match’s most controversial moment came on the hour mark. Another header back across goal caused a scramble in the area and as Emmerson Boyce went to clear he connected only with Junior Hoilett, but referee Mark Clattenburg waved away the appeals.
They kept up the pressure knowing that their league relegation loomed and Modeste tested Al-Habsi with a powerful effort.
Wigan was then denied a penalty kick. Moses sped past Orr but Clattenburg adjudged Moses to have dived after passing Pedersen in the Blackburn area.
With 10 minutes to go Blackburn brought on David Goodwillie for right back Bradley Orr as relegation crept ever closer with the score still at 0-0.
As soon as Rovers had made the substitution they almost fell behind. Moses’s shot was palmed out by Robinson straight to McCarthy, who couldn’t provide a lethal touch.
Wigan piled on a late surge as Boyce found space on the right hand side and crossed to the far post where Maloney headed over from just 6 yards.
With the away side well on top in the closing minutes it was no surprise when Wigan did eventually take the lead. Alcaraz climbed highest at the back post to power a corner kick at goal which was too hot for Robinson as Rovers’ Premier League status was taken away from them.