Roy Keane's men had dominated throughout the game, but ultimately paid the price for not scoring more goals while on top, and the visitors struck in the fourth added minute to leave them on the floor.
This was the third occasion in the last month that Ipswich have conceded in stoppage time - at Sheffield United where a 3-2 lead became a 3-3 draw and at Barnsley where a 1-1 scoreline became a 2-1 home win.
Keane has said his side are getting there and certainly this was a much improved display as they completely outplayed a Watford side who are on the fringe of the play-off race.
It was certainly hard to see how on this evidence as Town took just five minutes to go ahead. Liam Rosenior lobbed a free-kick into the box, Jon Walters got round the back to head across goal and the ball bounced up nicely for Gareth McAuley to head home.
Two minutes later it should have been 2-0 as Rosenior whipped in a superb cross which Pablo Counago completely missed four yards out, and Walters behind him could only guide onto the bar and away.
It didn't seem to matter at that stage as Ipswich continued to attack at every opportunity, with Liam Trotter skying over from 25 yards, Lee Martin shooting over from a Carlos Edwards pass and a Rosenior drive being deflected wide off Lloyd Doyley.
A Ross Jenkins back header from a David Wright long throw had to be tipped over by his own keeper Scott Loach before Jenkins had Watford 's first chance at the other end after 32 minutes but he fired well over.
Edwards shot across goal after robbing the dawdling Doyley and Leadbitter fizzed a 30-yard screamer just over before Don Cowie's cross-cum-shot floated just beyond the far post.
Malky Mackay clearly wasn't happy with his side and sent them out early for the second half, but it made little difference to the flow of the game, although the visitors did have the first chance when Adrian Mariappa headed wide from a Henri Lansbury free-kick.
Edwards had a great chance for a second goal for Ipswich when he was slipped in by Walters, but his firm drive from the edge of the box was turned away by the foot of Loach.
Sub Connor Wickham's back header dropped not far wide before McAuley nodded over after again being teed up by a Walters header from an Edwards cross.
Edwards had a speculative cross-cum-shot palmed over by Loach, who then made another fine save to turn away a free header for Wickham from Leadbitter's corner.
Loach also saved a Tommy Smith header as Ipswich continued to pile forward, and at one point Watford spent five minutes in their own half defending desperately a string of corners and long throws.
Unbelievably though Town's desperate bad fortune struck once again in stoppage time when a hopeful punt forward was weakly headed wide by Edwards and picked up by Graham, who crossed for Ellington to expertly volley home.