Wigan moved six points clear of the relegation zone after a scrappy win.
Filan was on loan at Doncaster earlier this season
The home side rode their luck at times - no more so than when keeper John Filan saved Nolberto Solano's penalty after Antoine Sibierski was fouled.
Ryan Taylor gave away the penalty but the defender quickly made amends when he whipped a free-kick past Shay Given to score his first Premiership goal.
Newcastle had had the better of the game before the penalty but after going behind they struggled in attack.
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It was a defeat that exposed Newcastle's frailties.
Having been so dominant in the early part of the game, Glenn Roeder's side proved incapable of mounting an effective response once they had fallen behind.
Oguchi Onyewu briefly glimpsed the Wigan goal but the American defender was unable to get a clean strike on the ball and his effort went over the bar.
That Newcastle were unable to score in that early purple patch was mainly down to Filan's heroics.
Given this was only the second time Filan, who went out on loan to Doncaster in October, had played for Wigan this season, the Australian keeper turned in an inspired performance.
As well as his penalty save, Filan twice denied Obafemi Martins and produced a superb stop to deny Damien Duff.
Arguably, Solano's penalty was too close to the 37-year-old Wigan goalkeeper but even so the Peruvian's effort had plenty of power and Filan needed a strong hand to keep out the ball.
Filan was soon in action again, getting down swiftly to his right to paw away a header by Martins.
Taylor was quick to inflict maximum punishment on Newcastle for that penalty miss.
The easy option for Taylor would have been to deliver a cross with the free-kick but the Wigan defender surprised everybody by bending a shot past Given into the top corner.
It was to Given's credit that Newcastle went in at the break only a goal down when he made a reaction save to turn away a Lee McCulloch header.
Before Taylor's goal, McCulloch had Wigan's two best chances but on each occasion the Scot fluffed his lines.
Late on Henri Camara's deflected shot almost looped over Given but the Magpies keeper quickly adjusted his feet to push away the ball.
Martins was Newcastle's most impressive player.
Before he cleverly backheeled the ball through to Sibierski to win the penalty, Martins had already gone close with a header and forced Filan into a save.
The Nigerian had also demonstrated his touch and vision by setting up Damien Duff with a deft pass that enabled the Republic of Ireland international to break clear, only to be thwarted by Filan's one-handed save.
Wigan manager Paul Jewell on goalscorer Ryan Taylor:
"Ryan broke his leg in a reserve game at Newcastle last year but he has worked ever so hard, and it's a big reward for his hard work.
"We can't do anything about other results, but if we win as many games as the bottom three, we'll be fine.
"I don't think it's necessarily three out of the current bottom four teams that will go down."
Newcastle boss Glenn Roeder:
"It was a nailed-on penalty and if we'd taken the lead then, we'd have gone on to win as we were on top and Shay Given had little to do.
"But we just didn't take the chances we created, or made the best of the good positions we got into.
"The second half wasn't a great spectacle, but it should have been all over by half-time."
Wigan: Filan, Taylor, Jackson, Boyce, Baines, Valencia (Camara 61), Landzaat, Skoko, McCulloch, Heskey (Kilbane 37), Folan.
Subs Not Used: Nash, Cotterill, Unsworth.
Booked: Filan, Taylor, Baines, McCulloch, Skoko, Camara.
Goals: Taylor 40.
Newcastle: Given, Taylor, Onyewu, Bramble, Huntington (Carroll 87), Solano (Milner 62), Parker, Butt, Duff (N'Zogbia 62), Martins, Sibierski.
Subs Not Used: Harper, Edgar.
Booked: Parker, Butt.
Ref: A Wiley (Staffordshire).