The Toon looked set to cling on to a point, despite having DeAndre Yedlin sent off in the second half.
But Doherty scored in the fourth minute of injury-time, nodding home the rebound after Diogo Jota had run from halfway and seen his effort saved by Martin Dubravka.
Nuno Espirito Santo’s side had earlier taken the lead after 17 minutes when Jota was given time and space in the box to control then slam home Helder Costa’s cross.
But the Toon levelled six minutes as Ayoze Perez flicked in Salomon Rondon’s centre.
Benitez’s boys were reduced to ten when Yedlin received a straight red for pulling down Jota when he was through on goal.
Yet they were fuming as Perez appeared to be elbowed in the box by Willy Boly and it went unpunished, before Doherty’s late sucker punch.
It was Wolves’ first win in 16 top-flight visits to St James’ Park as they moved into the top half.
While Newcastle are only three points clear of the drop zone having now lost seven of their nine home games this season.
The visitors went ahead when Costa cut inside from the right flank and swung in a left-footed centre.
And Jamaal Lascelles was caught in no man’s land, as the ball floated over his head to the unmarked Jota, who controlled with his chest inside the six-yard box and then volleyed in off Dubravka.
It was Jota’s second goal in as many games, after last season’s top scorer opened his account for this campaign in Wednesday’s win over Chelsea.
And you wondered if it was a move which had been thought up on the training ground, as boss Nuno celebrated by grabbing his entire coaching staff for a group hug.
Newcastle have lost every game in which they have fallen behind this season.
And Adama Traore, playing in the middle of the front three, was causing the Toon all sorts of problems early on.
He burst through the Toon’s midfield to thread through to Jota, who crossed for Costa, but Ciaran Clark got back in time to clear.
Newcastle, though, recovered from their shaky start and were level after 23 minutes.
The equaliser stemmed from a free-kick, which Rondon smacked against the bar from 25 yards.
It bounced back the wrong side of the line but Wolves only cleared as far as Rondon again.
And the Venezuelan whipped in a cross for Perez, who fantastically flicked over Patricio.
The Spaniard has been made a scapegoat by some supporters this season – and was ironically cheered off when he was subbed last week against West Ham.
So Perez’s celebration was clearly directed towards his critics, as he stood there with his fingers in his ears – just like he did when he scored the winner against Watford last month.
Benitez unusually made a tactical substitution at half-time, hooking Federico Fernandez and moving right wing-back Yedlin to become the third centre-half.
That was perhaps a way to combat Traore’s pace, as Yedlin is also lightning quick.
However, that change dramatically backfired 12 minutes into the second half as Yedlin took a terrible touch and was dispossessed by Jota before tugging the Portuguese down.
And referee Mike Dean was quick to brandish a red card to the American, adjudging that Jota would have got a shot away before Lascelles could cover.
Wolves boss Nuno then brought on Morgan Gibbs-White – who was unlucky to be benched after starring against Chelsea on his full Premier League debut – and Jimenez.
And it was Jimenez who almost grabbed the winner as, from a speedy counter led by Costa, he cut inside and then rattled the bar.
Wolves came close again as, from another breakaway, Doherty’s left-footed curler was superbly saved by Dubravka.
But Newcastle were furious as the move came after Perez was floored by the elbow of Wily Boly, who was lucky not to be punished.
And they were even more angry in injury time, as Jota was allowed to run unchallenged and get a shot away, with Doherty on hand to head home the winner.
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