The match seemed likely to end goalless before Nugent’s late intervention saw Boro go second in the table, two points above Brighton.
For Steve Bruce’s Hull, the loss continues their run of poor form that has seen them score just four goals in nine Championship matches.
The Tigers will be left ruing their missed late chances, with Elmohamady guilty of missing a great opportunity after Abel Hernandez’s initial effort was blocked out to him.
Middlesbrough, who will drop back down to third if Brighton win at MK Dons on Saturday, travel to QPR after the international break while Hull will host Bristol City.
Good to be back
It has been a strange week on Teesside, with many expecting that Karanka would leave his position after an incident at the club’s training ground prompted him to walk out before Sunday’s loss at Charlton.
On Monday it was announced that the Spaniard would be staying at the Riverside Stadium and said: “I think the club and me had everything clear. The club never thought to sack me and I never wanted to leave.”
The Boro supporters got behind Karanka and their team from the start and, ultimately, they were rewarded.
Former England midfielder Steve Stone on BBC Radio 5 live:
“Hull will be devastated that they have lost that game.
“All of the Middlesbrough supporters will come together and forget about what happened last week now. That Nugent goal could change their season.
“I spoke about momentum before the game and the confidence that comes from winning that game is huge.”
Middlesbrough head coach Aitor Karanka: “I think it has been the best way to finish the day. The day, the week, everything – I couldn’t have imagined to finish the game in that way.
“I told the players before the game that it was going to be a really emotional game because of a lot of rumours, a lot of things had happened.
“I said yesterday in the press that today was a good day to show everybody how big this club is, how great this crowd is and how good these players are when they play in the way that we have to play.
“For that reason I told them after the game, and I want to say to everybody, just one thing today: thanks.”
Hull manager Steve Bruce told BBC Radio Humberside: “I couldn’t fault the performance.
“We’ve had the two outstanding chances in the game, and in a game of this magnitude we’ve got to take them.
“It’s cost us, because at the end we had a lot of tired bodies and we’ve been punished. We can’t keep relying on a clean sheet because things happen like they did today.”