The ex-Newcastle striker had not found the net in his previous 12 outings, but popped up in the 90th minute to turn in a low cross from Carlos Edwards from six yards.
The effort made up for an earlier bad miss when Chopra sent a 69th-minute shot over the crossbar from 12 yards.
Paul Jewell's Tractor Boys had lost their last five matches against the Hornets - and were without a victory over their Championship rivals in their previous 15 meetings.
But they held the upper hand for long periods.
The Hornets, now under the stewardship of Italian Gianfranco Zola, had won their opening two matches of the season, a 1-0 success over Wycombe in the Capital One Cup and a 3-2 victory away to Crystal Palace in the league, but it was Ipswich who had the better of the first half.
A right-footed 30-yarder from Lee Martin was superbly tipped over the crossbar by Hornets keeper Manuel Almunia in the third minute.
Both Martin and striker Michael Chopra then sent edge-of-the-box drives flashing narrowly wide, before a Jay Emmanuel-Thomas 25-yard free-kick flew past Almunia's left-hand upright.
And Emmanuel-Thomas drove another 20-yard shot wide as Ipswich continued to have the edge in terms of possession.
After 29 minutes Massimo Luongo produced a right-footed shot from outside the penalty area but again Almunia was not called upon to make a save.
But five minutes later Almunia was alert to punch clear an inswinging free-kick from Martin.
Ipswich also had the first real effort of the second half, the impressive Emmanuel-Thomas lashing another left-foot shot from outside the penalty area wide of the target.
Almunia then pulled off a good save in the 55th minute to keep out Luongo's left-footer.
Watford needed to try and gain the initiative and Zola opted to bring on Chris Iwelumo for the ineffective Joe Garner, and the big substitute immediately created an opening for Almen Abdi, who fired over the crossbar from 12 yards.
After 65 minutes a shot by Matej Vydra from the left-hand side of the penalty area was well blocked by Ipswich midfielder Luke Hyam.
Ipswich goalkeeper Scott Loach, who had left Watford for Portman Road in the summer, was called into action four minutes from the end of normal to deal with a 20-yard shot from Matej Vydra.
Ipswich had conceded 45 goals on their Championship travels last term, more than any other club in the division, but Loach was all smiles on the final whistle as he gained a clean sheet on his return to Vicarage Road.
