Roberto Martinez's side eased their relegation fears with an important win as goals either side of half-time saw off a disappointing Reading.
Wigan went close early on when Franco Di Santo forced a great save from Adam Federici following a solo run.
It looked as that would be the only real chance of the half until Kone dug a shot out to bring another good save from the Royals' keeper.
Kone did beat Federici with two minutes of the half remaining, prodding the ball home from close range after Reading failed to clear a corner.
The striker then grabbed a second two minutes later as he raced onto a ball forward from Jean Beausejour and chipped the keeper to make it comfortable at the break.
Figueroa added a third for the visitors three minutes after half time, playing a neat one-two with Di Santo before slotting the ball through the legs of Federici.
Reading's afternoon got worse when they were reduced to 10 men, Pavel Pogrebnyak given his marching orders for a late challenge on Figueroa.
Wigan went close to a fourth, Figueroa bringing a great save out of Federici, before Jordi Gomez's shot with the outside of his boot was kept out by the Australian.
The win sees the Latics move out of the bottom three, ahead of Aston Villa on goal difference, while Reading drop back into the relegation zone.