The Canaries were going in to the tie at Vicarage Road having scored just once in their last four games and found themselves two goals behind to Watford following fine strikes by Javier Acuna and Davide Faraoni either side of half-time.
But Hooper, who made his long-awaited debut for Norwich from the bench in Saturday's 1-0 loss to Aston Villa, took the game to extra time with a 95th-minute header after Josh Murphy had pulled one back.
The 25-year-old then sealed the win for Norwich when he slotted home Leroy Fer's tremendous pass with just five minutes of extra-time remaining leaving Hughton not only pleased with his performance but also with his fitness.
"He is a finisher," the Norwich boss said of his summer signing.
"I'm probably as delighted that he has got 120 minutes under his belt than I am with the goals. He is used to scoring but with all strikers it is about the service they get and showing a little bit of quality when they can.
"Both goals showed great movement, a super ball from Leroy Fer for the third. Even in that second half of extra time I was looking at how he was running and he was fine."
Academy graduate Murphy had travelled with the Norwich squad and made an instant impact as he thrashed home a 76th-minute screamer that set the Canaries on their way to a superb comeback win.
Hughton revealed he had always planned to utilise the young winger at some point during the game but had resisted the temptation to throw him in from the start after the disappointment of the weekend's result.
"With Josh I thought he would certainly benefit from the open spaces," he said.
"My intention was to always involve him and I thought long and hard about starting him and perhaps the result on Saturday changed my mind but I'm delighted he was in the squad and produced the goal that got us back in the game."
Watford manager Gianfranco Zola was left deflated by the defeat but believes his players will have learnt from the experience of facing top-flight opposition.
'It is a crushing feeling of course," he said.
"We were winning a game and deserving to against Premier League opposition. But this game is about the attention you put in at crucial moments and that is the learning side for us."