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 television replays suggested he had a case - but referee Keith Hill was unmoved.
And moments later Crofts equalised as Watford, last season's beaten play-off finalists, missed the chance to climb up to fourth in the Sky Bet Championship.
Brighton could argue Forestieri should not have been on the pitch by then but his first-half lunge on home goalkeeper Tomasz Kuszczack was mistimed rather than malicious, and earned him only a yellow card.
Watford had taken the lead after only four minutes when Sean Murray took aim from 25 yards.
His shot took a wicked deflection off Seagulls full-back Stephen Ward to send the ball spinning past Kuszczak and into the net.
Lewis McGugan almost made it two four minutes later but his curler flew narrowly wide.
Patched-up Brighton were missing seven first-teamers through injury but still had livewire winger Will Buckley to lead their search for an equaliser.
They thought they had found one after a quarter of an hour when Ashley Barnes headed Buckley's cross powerfully towards the top corner.
But Manuel Almunia pulled off a spectacular diving save to claw the ball out and Barnes smashed the rebound into the side-netting.
Moments later Craig Conway got on the end of another Buckley cross only to plant a free header wide.
Just before the interval Conway's cross found Buckley, who scooped the ball back into the danger area but Barnes was unable to convert.
After the restart came the goal-line incident which left Forestieri and Watford frustrated - and they were distraught in the 53rd minute when a half-cleared corner fell to Crofts, who swivelled to crash the ball past Almunia.
Both sides had chances to win it with Forestieri - inevitably - going closest for Watford when his header came back off the base of a post, while Crofts forced another fine save from Almunia with a fierce drive late on.