Nolberto Solano brought Everton's unbeaten Barclays Premiership run to an abrupt halt to hand Newcastle a fourth victory in five games under caretaker boss Glenn Roeder.
The Peruvian slid home Charles N'Zogbia's 64th-minute cross to open the scoring, and produced a stunning finish 14 minutes from time to take his goal tally for the season to five.
It was a strike of which injured skipper Alan Shearer would have been proud as David Moyes' men tasted defeat for the first time in eight league outings and only the second in 12 in all competitions.
But despite Turkish midfielder Emre twice having to clear David Weir headers off the line before the break, the Magpies were good value for their victory as they kept a fourth clean sheet under former defender Roeder to delight the bulk of a crowd of 51,916.
With Shearer's name once again missing from the team-sheet, the home fans arrived wondering where the goals were going to come from against a side which had won six and drawn one of their last seven league games.
On Wednesday night, the Magpies enjoyed more than their fair share of possession against Charlton, but failed to create enough chances to win the game, Shola Ameobi squandering the best of the 14 minutes from time.
Caretaker boss Roeder again asked Emre to provide the support to lone striker Ameobi but, in the event, his most crucial contributions in the opening 45 minutes came on his own goal-line.
Twice the former Inter Milan star hacked Weir headers off the line as a makeshift Newcastle defence, which was coping reasonably well in open play, lost their bearings from Mikel Arteta's corners.
It was the Spaniard too who forced Shay Given into his only save of the half with a minute remaining, the Irishman tipping a dipping free-kick over the bar as it sped towards him on a bitterly cold Tyneside wind.
However, for all that the visitors created three excellent chances to take the lead, the home side had more than their fair share of possession and might themselves have gone in ahead at the break.
Four opportunities fell to Lee Bowyer alone as he dragged a left-footed shot just wide, saw another effort deflected over and then fired across goal and headed over the top.
But Newcastle's best chance came in first-half injury-time when N'Zogbia escaped from Joseph Yobo on the left and squared for Solano, whose shot was palmed away by loan signing Sander Westerveld in the Everton goal.
But having finished the first half strongly, the home side started the second beset by a strange lethargy as the visitors pinned them back again.
That changed when Scott Parker and Solano combined well on the edge of the Everton box before the Peruvian found Ameobi, although his shot was charged down.
As play switched quickly from end to end, Leon Osman saw the whites of Given's eyes two minutes later, but his right-footed snap-shot flew wide of the keeper's left post.
There was little to choose between the sides, although Bowyer might have done better with a first-time effort after N'Zogbia had cut out Yobo's clearance and played the ball into his run on 59 minutes.
Elliott had to block a Tim Cahill shot after Celestine Babayaro had neglected his defensive duties, but the breakthrough finally came at the other end with 64 minutes gone.
Emre did well on the left to hold the ball up and the lay it into N'Zogbia's path, and the Frenchman cut into the box before delivering the perfect low cross for Solano to slide home the opener from close range.
It could have been 2-0 within seven minutes when, after Westerveld had prevented Bowyer from finishing off a flowing attack, Parker thumped a volley just wide from the resulting corner.
Tim Cahill, who had earlier been injured in a challenge with Parker, was replaced by Lee Carsley with 16 minutes remaining, but the home side were pushing to kill the game off.
And they did so in superb style with 14 minutes remaining when Bowyer rolled the ball into Solano's path and the South American curled a shot beyond Arteta with the outside of his right foot.
Yobo might have pulled one back with an 86th-minute header from Arteta's free-kick, and James Beattie fired wide at the death, but the clean sheet was just reward for a committed team performance.
Teams:
Newcastle Given, Ramage, Boumsong, Elliott, Babayaro, Solano,Parker, Emre (Clark 79), N'Zogbia (Pattison 90), Bowyer, Ameobi.
Subs Not Used: Harper, Faye, Chopra.
Booked: Parker.
Goals: Solano 64, 76.
Everton Westerveld, Yobo, Stubbs, Weir, Nuno Valente, Osman,Arteta, Cahill (Carsley 74), Davies, Kilbane (McFadden 68),Beattie.
Subs Not Used: Ruddy, Naysmith, Vidarsson.
Booked: Cahill.
Att: 51,916
Ref: G Poll (Hertfordshire).