Stoke will feel incredibly hard done by after deservedly being ahead through Oussama Assaidi's stunning opener, as Newcastle toiled in front of an expectant home crowd.
But the first half ended with Glenn Whelan, Marc Wilson and manager Mark Hughes being sent off for the visitors, while Loic Remy made up for a penalty miss by hitting the home side's equaliser.
In the second half, Newcastle understandably dominated with their two-man advantage.
Goals from Yoan Gouffran, a second from Remy and one from Yohan Cabaye ensured more happy holidays for Alan Pardew's men, as they jumped back above Manchester United into sixth place.
After a cagey opening half an hour, it became clear that it would take something special from either side to break the deadlock at an icy St James' Park.
It was visitors Stoke, who have just one league win on their travels this season, who grabbed the first against their much-fancied opponents, and it was well worth the wait.
Charlie Adam was the creator, working the space to lay off at the feet of Liverpool loanee Assaidi.
The skillful Moroccan, whose last goal was an excellent winner in the 3-2 victory over Chelsea earlier this month, continued his streak of stunning strikes after cutting inside and curling in a sublime effort over the head of Newcastle keeper Tim Krul.
With Stoke in the driving seat and cruising, it looked as if it would take quite something to drag a flat Newcastle back onto level terms.
Within a 10-minute period late in the first half, Stoke's nightmare came true however, culminating in ending the half with just nine men on the pitch, as their comfortable lead was crushed.
Whelan, who was first booked for a rash challenge on Moussa Sissoko, received his marching orders five minutes later after felling Cabaye.
Replays showed that referee Atkinson's decision was perhaps harsh, a view clearly shared by Potters boss Hughes who received marching orders himself.
A couple of minutes later, Stoke were another man down.
With the insipid Remy slipped in behind the defence, Stoke centre-back Wilson was adjudged to have dragged down the Frenchman in the area.
Atkinson produced another red as he pointed to the penalty spot, giving Newcastle, who, in truth, looked poor and bereft of ideas for 40 first-half minutes, a huge lifeline to draw level.
Remy wasted the chance however as Thomas Sorensen - starting in place of the injured Asmir Begovic - saved his penalty and cleared.
Stoke broke forward quickly, and, after cries for a handball against Mike Williamson were controversially waved on by Atkinson, Newcastle struck on the counter.
The impressive Hatem Ben Arfa, starting his first game since October, slipped the ball out to Remy, who cut inside before his deflected effort found a way through for the equaliser.
The visitors understandably struggled to deal with the numbers game in the second half, and the home side quickly capitalised.
Ben Arfa's cross was poorly dealt with by a beleaguered Stoke defence and, after Sorensen's failed punch, Gouffran put Newcastle into the lead on 48 minutes
Not for want of trying, Ben Arfa couldn't quite get on the scoresheet himself, despite two incredible solo runs which both ended in his efforts smashing back off the woodwork.
For all Stoke's efforts, the game was always slipping away from them however, and Remy's header after Sissoko's miscue from a Mathieu Debuchy cross on 55 minutes was followed up by a great team goal from Yohan Cabaye 11 minutes later.
The icing on the cake came as second-half substitute Papiss Cisse smashed home an 80th minute penalty won by Ben Arfa, completing a miserable Boxing Day with plenty to bemoan on the trip home for Hughes and his side.