Wolves boss Nuno Espirito Santo said the red card "changed the game" and admitted his side were "lucky to beat them in the end".
"It's too difficult for me to judge because I'm on the other side of the pitch," he added.
Newcastle forward Perez said: "I'm not saying if it's a red card or not, but I'm pretty sure if it had been at the other end it wouldn't have been a red."
Newcastle felt they should have had a penalty when Boly appeared to elbow Perez as he jumped for a header in the box.
Play was allowed to go on and Wolves almost scored from the resulting counter-attack, keeper Martin Dubravka diving to his right to keep out Doherty's curling effort.
Perez received treatment on the pitch for a bloody nose.
"I don't know what we have to do to get a penalty but we just have to keep going," said Perez.
"The guy elbowed me really hard straight in my nose, but the referee said it was the ball that hit me, not the elbow, even though I was bleeding."
Benitez said: "It's so obvious. The red card and the elbow in Perez's face - we need the VAR."
This victory came four days after they ended a run of seven league games without a victory by beating fourth-placed Chelsea 2-1.
They were made to work hard by Newcastle, who had the upper hand before Yedlin's dismissal.
But Jota was again influential, scoring his second goal in as many weeks and winning the free-kick which led to the sending-off. It was also his shot that was palmed into Doherty's path late on.
Doherty had forced a diving save from Dubravka and Raul Jimenez hit the crossbar, before the former struck the decisive blow as the clock ticked down.
Victory was Wolves' second in succession in the league - the first time they have secured back-to-back wins since early October.
For now, they can celebrate a place in the Premier League's top 10.
Newcastle have now failed to win their past three Premier League games, but could easily have taken all three points against Wolves.
They were on the front foot from the start, Rondon forcing a save from Rui Patricio with a fizzing half-volley moments after kick-off before smashing the underside of the crossbar with a testing free-kick.
As well as having 60% of possession in the first half, Newcastle had 10 shots, four on target - a tally they have bettered only once this season.
But the game changed when Yedlin was sent off as Newcastle slipped to a seventh defeat in nine home games.