The result wasn't a shock in the context of the club's respective league positions, but it was when judged on the supposed strength of the teams the two mangers put out.
Wolves boss Glenn Hoddle made seven changes to the side which drew with Leicester at the weekend, but still included the likes of Kenny Miller, Colin Cameron and Jody Craddock.
By contrast Adrian Boothroyd, who also made seven changes, started with a largely youthful looking team and gave senior debuts to academy players Toumani Diagouraga and Francino Francis.
It looked like Wolves' greater experience would tell when they bossed the opening stages and capitalised on their good start after 12 minutes.
The visitors were awarded a rather fortunate free-kick outside the right edge of the area but the Watford defence was caught cold as Mark Davies drove the ball in low and the returning Miller attacked the near post and stabbed home post Alec Chamberlain from close range.
The Hornets then re-organised tactically, matching Wolves' 4-3-3 formation, and this enabled them to get a foothold in the game, although decent chances were at a premium for both sides for most of the first half.
However, in injury time Carlisle rose above his marker to head a Anthony McNamee corner firmly past Stefan Postma.
Boosted by the equaliser, Watford's youngsters grew in confidence after the break but scoring opportunities continued to be few and far between, although George Ndah should have done much better when a Miller cross presented him with a clear chance at goal but the substitute shot badly wide.
Both sides had chances to avoid the extra half hour in the closing stages of normal time.
First Watford replacement Joel Grant fired a rising drive straight at Postma, while at the other end Chamberlain had to scramble across his goal to deny Cameron from close range.
The veteran 41-year-old Watford keeper then excelled in the opening period of extra time, showing superb reflexes to tip over an Ndah header.
But Watford produced the moment that mattered when Matthew Spring swung over a free-kick from the left and Carlisle got across the face of the defence to head home his second of the night.