Goals from Fabricio Coloccini and Andy Carroll, both scored within the first five minutes of the start of each half, put the Magpies in the driving seat before a late Will Hoskins strike gave the Hornets a late glimmer of hope.
Toon boss Hughton was delighted with the win and said: "It's a tough place to come.
"They are side that have got a lot energy, they played very well at St James' Park earlier in the season.
"The first goal obviously set us off and we had a period in the second half where we were very comfortable and probably the only disappointing note of the afternoon was conceding the goal when we did."
Watford suffered only their second defeat in nine games at Vicarage Road and manager Malky Mackay felt his side deserved better.
The Hornets boss said: "When you look at the balance of play I think that we deserved something out of the game today.
"We were playing the top team in the league and I think we coped well with the fact they decided to go long today. We won a lot of ball back off that and I thought we kept possession well and dominated play at times.
"When you're looking out there at the pitch, at times it looks awful and we didn't just resort to getting it and kicking it.
"I think there were areas of the pitch where we exposed them and we managed to get into forward areas, still in good possession of the ball after four, five, six passes and that gave us good position.
"I think it was our final ball that let us down today because we certainly got into the forward areas well."
The visitors took the lead when a free-kick from the left was not dealt with and Carroll headed back across goal for Coloccini to beat Scott Loach at his near post with a header from close range.
Watford's hopes of getting back into the contest were further dented within five minutes of the start of the second half
when, from Newcastle's first corner, Danny Guthrie clipped the ball towards the near post and Carroll thumped a header past Loach.
The Hornets never gave up though, and their efforts were rewarded in injury-time when a Heidar Helguson shot appeared to be blocked by Kevin Nolan's hand, but the ball broke nicely for substitute Hoskins to confidently beat Steve Harper.