The Gateshead-born striker teed up Fabricio Coloccini for the opening goal and then got on the scoresheet himself after the break.
Will Hoskins replied late on for Watford, prompting some unsavoury squabbling in the Newcastle ranks, but the visitors held on.
And with Nottingham Forest, who kicked off in second, dropping points, Chris Hughton's side were able to take another huge stride towards promotion back to the Barclays Premier League.
It could have been so different had Watford made the most of an opportunity in the first minute when Danny Graham pulled the ball back for Don Cowie, but the midfielder hurried his shot and lifted it over the crossbar.
Jon Harley then got a sight of goal for the hosts but his effort was comfortably dealt with by Steve Harper.
Instead Newcastle made the most of their first chance in the fourth minute, when Watford failed to clear Danny Guthrie's free-kick.
Carroll headed the ball back across the penalty area and Coloccini rose above Adrian Mariappa to plant a downward header past Hornets keeper Scott Loach for his second goal for the club.
Jonas Gutierrez could have doubled the advantage but he fired wide and Carroll put a header the wrong side of the post.
But on a heavy pitch, Newcastle were making heavy weather of adding to their lead.
And with Watford threatening an equaliser, ex-Vicarage Road defender Mike Williamson was fortunate to escape with a booking when he pulled down Heidar Helguson as the striker attempted to run through on goal.
But after the break Newcastle finally got their two-goal cushion courtesy of another set piece. Guthrie clipped a corner towards the near post where Carroll got ahead of centre-half Jay DeMerit and nodded the ball past Loach.
It was Carroll's 11th goal of the season and capped an impressive performance from the 21-year-old.
Watford, to their credit, kept going and Adrian Mariappa's cross found its way to the feet of substitute Stephen McGinn, but the youngster sliced wide.
They grabbed one back in stoppage time through substitute Hoskins, who looked offside when he finished from close range.
The goal prompted a frank exchange of views between Williamson and Alan Smith in the Magpies' penalty area, but they were all smiles when the final whistle blew moments later.