The striker scored a last-minute winner to send Roberto Martinez's side to within three points of safety, although they were lucky not to have had Callum McManaman sent-off for an earlier tackle which saw Massadio Haidara stretchered off.
Jean Beausejour handed the hosts the lead, only for Davide Santon to level matters before the Ivorian's dramatic late winner.
Wigan's young goalkeeper Joel was forced into the first meaningful save of the afternoon as he sprang across his line to handle Sylvain Marveaux's point-blank header from an inswinging corner.
And after some more assertive pressure from the hosts, they eventually broke the deadlock on 18 minutes with a well-worked goal. McManaman showed quick fleet of foot to burst past Haidara down the right before delivering a cross to the back post where Davide Santon made a mess of his clearance that allowed Jean Beausejour to sweep in his first goal for the club.
The hosts were lucky not to have McManaman sent-off soon after though as substitute Haidara was stretchered off following a horror tackle by the forward. Referee Mark Halsey failed to see the incident from where he was standing, therefore did not even brandish a card.
Goalkeeper Rob Elliot was called into action as he parried away Shaun Maloney's curler from just inside the area as the Latics pressed forward in search for a second.
Just before the break they had a real opportunity to do that as James McCarthy broke through the middle of the park and seemed to be in the clear until Jonas Gutierrez came sliding in to make an excellent last-ditch tackle.
The second half started in a real frenzy with McManaman's goalbound effort well blocked by Mapou Yanga-Mbiwa before Cisse ballooned his effort over the crossbar from close-range.
The game tipped in the Magpies' favour with 18 minutes remaining as they restored parity to delight the away contingent. Cisse found Santon with a well-timed pass and the Italian scored his first senior goal with a strike which flew under the legs of Maynor Figueroa and past Joel.
With a couple of minutes remaining Cisse's toe-poke towards goal was touched wide before Wigan grabbed a dramatic winner thanks to Kone.
A corner from the right caused mayhem in the box with Newcastle players appealing for handball on Figueroa, but the striker was johnny on the spot to slot the ball into the roof of the net and seal a vital home win.