Diogo Jota’s close-range finish put the visitors ahead early on at St. James’ Park, but Ayoze Pérez’s header levelled matters 22 minutes in.
Full back DeAndre Yedlin was dismissed for hauling down Jota after the break, but it took until the fourth of five added minutes for Nuno Espirito Santo’s side to break United down, as Doherty nodded in the winner.
It was harsh on Rafa Benítez’s charges, who turned in a spirited display only to be undone in the game’s dying moments.
They had begun brightly, with Rondón testing Rui Patricio with a low volleyed effort from Mo Diamé’s cross, but it was Santo’s men who seized the advantage with quarter of an hour gone. It was a goal Newcastle will feel was preventable, as Doherty found space on the right before picking out the unmarked Jota in the middle. The Portuguese winger had time to take a touch before slotting the opener past Martin Dúbravka from eight yards out.
The visitors’ pacey frontman Adama Traore was keeping Jamaal Lascelles and Federico Fernández occupied, but falling behind didn’t seem to deter United. It took just seven minutes for them to level the score in style; Rondón’s sweetly-struck free kick cannoned off the underside of the crossbar and was cleared, but when the Venezuelan picked up the pieces and bent a fine cross into the centre, Pérez was perfectly placed. The Spaniard’s glancing header flew past Patricio and lifted the 50,000-strong crowd midway through the half.
Save for a deflected Diamé drive, there were few more openings before the break, when Benítez opted to introduce Javier Manquillo in place of Fernández. With Matt Ritchie at left wing-back and Manquillo operating on the right, Yedlin moved into a more central defensive position alongside Lascelles and Ciaran Clark as United sought to contain the speed of Traore.
But another tactical reshuffle was required just ten minutes into the second half. Jota stole possession from Yedlin on the left and, as he bore down on goal, the American pulled him down. He was shown a straight red card by referee Mike Dean, and the hosts were left to play the final half hour with ten men.
Wolves looked to take advantage, sending on frontman Raul Jimenez and Morgan Gibbs-White, but the numerical deficit didn’t pose any immediate problems for Newcastle. Diamé’s cross was cleared as far as Pérez but, after bringing the ball down, his shot was too high.
In the final quarter of an hour, though, Wolves began to probe for a winner. A quick counter-attack left Jimenez with a shooting opportunity, but his strike thumped against the crossbar – just as Rondón’s first half attempt had – and stayed out.
Then, with Pérez lying injured in the Wolves box, the visitors launched another attack. Jota’s lay-off found Doherty running onto it, but Dúbravka did superbly to get down and palm away the Irishman’s powerful drive.
The United stopper held onto Jimenez’s header soon after and Clark produced a fine block to prevent Gibbs-White from testing the goalkeeper, but deep into injury time, Wolves snatched all three points. It was cruel on Newcastle, who had fought valiantly after Yedlin’s dismissal but after Dúbravka had kept out Jota’s effort, Doherty pounced, heading in the rebound to condemn the Magpies to defeat.