Town were left to suffer the bitter taste of defeat as Wigan's Cook served up a second-half treat for the home side.
In truth, the Latics' pressure deserved three points but it was the manner of the winning goal that proved hard for the visitors to swallow.
Referee Trevor Parkes penalised Adam Willis for a perfectly good challenge on the edge of the area and loan signing Paul Cook thumped the winner past Bart Griemink.
Town's players were rightly furious about the decision but Wigan would have felt anything less than a victory would have been scant reward for their efforts.
The Town defence repelled wave after wave of Wigan attacks but had it not been for the heroics of Griemink then defeat could have been a lot heavier.
The Dutchman made a number of stunning stops to keep his side in the game as Town struggled to keep Paul Jewell's men at bay.
Despite Wigan's lowly league position, the fear was that it was merely a matter of time before their expensive squad came good.
Typically, they chose the visit of Town to produce the goods.
Roy Evans' men struggled to create clear cut chances and spent far too much of the game pinned back in their own half.
Eric Sabin and Danny Invincible were well shackled by Wigan's Matt Jackson and Arjan De Zeeuw but the Town strikers lacked the sort of service needed for them to make an impact.
But it could all have been so different had Town capitalised on a bright opening.
The visitors forced a corner after just 40 seconds following a wayward back pass.
Wigan failed to clear their lines and as the ball fell to Matt Hewlett, the midfielder arrowed a shot wide when handily placed.
Hewlett was in the thick of the action again six minutes later.
Wayne Carlisle fed Sabin down the right and his cross was nodded down for Hewlett. Sadly the former Bristol City man scuffed his shot and the chance was gone.
The home side began to haul themselves into the game and the powerful Simon Howarth seemed to relish his battle with former Coventry team mate Adam Willis.
Cook orchestrated matters in midfield alongside Paul Dalglish.
The young Dalglish, watched by dad Kenny, is not in the class of his father, but still had more than enough tricks in repertoire to keep Willis and co on their toes.
Howarth tangled with David Duke inside the box but the referee waved away cries for a penalty.
Sabin almost played Invincible through in the 10th minute but Jackson stretched out a leg to whip the ball off the Aussie's toes.
Invincible was unlucky six minutes later when he timed his run to perfection but Steve Robinson overhit his through ball just a fraction and allowed Derek Stillie to race out and smother the striker's effort.
Andy Liddell warmed Griemink's gloves with a 17th minute strike from the edge of the box but the Latics were desperately unlucky not to take the lead two minutes later.
Dalglish swivelled on the edge of the box and hammered a terrific shot against the underside of the crossbar.
Town failed to heed the warning and the home side began to tighten the screw.
Wigan began to string their passes together and a fine move in the 27th minute involving Kenna, Liddell and Dalglish ended with Howarth planting a header on to the roof of Town's net.
On the rare occasions Town managed to get into the final third, the ball would not drop kindly and Sabin's acrobatic effort in the 32nd minute lacked the power to beat Stillie.
The Latics had a stronger penalty claim turned down moments later when skipper for the day Andy Gurney brought down Liddell.
As half-time approached, the visitors raised their game and David Duke should have done better with a 42nd minute opportunity.
Matt Heywood crossed from the right but as the ball dropped to Duke on the edge of the box, the Scotsman appeared to slip and the ball slipped away just as he prepared to pull the trigger.
Town had a penalty shout of their own turned down when Invincible crashed to the floor but the visitors could be fairly satisfied at getting through to the break with their goal in tact.
Town's defenders could rightly argue that the Wigan attack had largely played across them in the first-half but the Latics looked more menacing after the interval.
Griemink made a wonderful save from Jackson's close range header in the 51st minute.
The Town fans breathed a sigh of relief two minutes later when Howarth flicked Liddell's cross wide but it began to look rather ominous for Roy Evans' side.
Bobby Howe replaced the ineffective Sabin in attack but it was Sabin's strike partner Invincible who should have given the visitors a priceless 63rd minute lead.
The 22-year-old nipped between Jackson and De Zeeuw but seemed to knock the ball a touch too far and Stillie came out well to rescue his side.
Town could not afford to waste the few opportunities that came their way and they were made to pay with a little over 20 minutes remaining.
Willis made what appeared to be a perfectly good tackle on Liddell but Mr Parkes seemed to disagree.
The defender's furious reaction suggested he felt a serious injustice had taken place.
But however questionable the decision, it proved fatal to Town's hopes of prising a point from the contest.
Cook whipped the ball into the net, with the help of a deflection, and the points were all but secured.
It should have been 2-0 seconds later as Howarth raced clear.
But with Liddell screaming for the pass that would have presented him with a simple tap-in, Griemink stretched out an arm to thwart Howarth.
Scott Green's fine 75th minute run ended with the former Bolton man firing well over the bar.
Mark Robinson made way for Paul Edwards and the Mancunian enjoyed a solid last 15 minutes, offering a touch more attacking threat.
His cross from the left in the dying seconds caused panic in the Wigan box but the ball was scrambled clear before a red shirt could pounce in the six yard box.
Griemink then came to Town's rescue again to thwart Howarth as Wigan struggled to finish off their visitors.
Sol Davis also returned to the action as a late substitute as Town piled forward in a last-gasp bid to snatch a point.
Sadly the visitors could not take advantage of the five minutes of added time although Gurney clearly felt he had been impeded by De Zeeuw inside the box.
But Mr Parkes was not in the mood to do Town any favours and Gurney's protests were dismissed.
The final whistle brought defeat and probably a wish from the Town camp that the referee would locate Wigan Pier and throw himself off it.
But defeat has to be kept in context. Disappointing but not a complete disaster.
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