The Hornets were leading through Sean Murray's early deflected strike and were convinced they had scored another just after the interval through Fernando Forestieri.
Brighton captain Gordon Greer miscontrolled the Italian's shot and sent the ball rolling towards goal, the defender eventually hacking it clear from behind the line.
Forestieri argued long and hard with the linesman that the ball had crossed - and replays suggested he certainly had a case - but referee Keith Hill did not signal a goal and, unlike in the Premier League, he had no option to consult video technology.
And moments later Andrew Crofts equalised as Watford, last season's beaten play-off finalists, missed the chance to climb up to fourth.
"There's no doubt about it, it's definitely a goal,"said Hornets boss Zola.
"Everyone has seen it apart from the referee and the officials. That is the disappointing part, the goal did not happen in a crowded area, there was only the player, the ball and the line and it has not been seen.
"I am disappointed because it would have given us three points.
"In a championship in which so much money is involved - they say it's £120million for the teams that go up - it (technology) would help the officials keep everything under control.
"If it is something we can use to make the game better why not? After today I would like it to be at least considered."
Seagulls chief Oscar Garcia was, perhaps unsurprisingly, less convinced the ball had crossed the line.
"From my position it was impossible to see," he said. "I didn't ask Gordon about it."
Forestieri was the central figure throughout the match, escaping a red card for a first-half lunge on Brighton keeper Tomasz Kuszczack and hitting the base of a post with a header late on.
The striker also teed up Murray's opener, although that 25-yard strike owed a lot to a big deflection off Stephen Ward to take the ball past Kuszczack and into the net.
But moments after the goal-line controversy Brighton went down the other end and scored, Crofts swivelling to smash home a half-cleared corner.
Crofts also had a chance to win it late on with a shot which was superbly kept out by man-of-the-match Manuel Almunia, who had also acrobatically denied Ashley Barnes in the first half.
"We played well in the first half and deserved more than to go in 1-0 down," said Garcia.
"In the second half, they had chances and so did we.
"It's not the first time the opposition has scored with a deflection against us this season, but I'm happy with the reaction of my players and how they played against one of the best teams in the Championship."