Paul Wotton and Stevie Crawford both found the net as the Pilgrims recorded a shock 2-0 win at the JJB Stadium.
Wigan, who were missing star striker Nathan Ellington, had been undefeated for longer than any other side in all four English divisions.
Despite the defeat the Latics remain top of the Championship tonight, but their lead at the top has been slashed to three points following Ipswich's 2-0 win at Burnley.
Darren Bent scored his sixth and seventh goals of the campaign at Turf Moor to give the Tractor Boys a comfortable win.
Ipswich's success means that third placed Reading were unable to close the three point gap between them and the top two.
But the Royals put daylight between themselves and fourth place with victory this afternoon. Their win put them three points clear of Sunderland who were beaten 2-0 at Millwall last night.
Below them, West Ham leap-frogged QPR into fifth with a 2-1 win over the Hoops at Upton Park. Marlon Harewood scored both goals for the home side.
Championship Results - Saturday 6th November:
Brighton & Hove Albion 1 Crewe Alexandra 3