The promotion-chasing Hornets were on track to make it five home wins from six games when Cristian Battocchio dinked the ball over Matthew Gilks midway through the first half.
However, Gianfranco Zola's side were unable to push on after the break and the visitors equalised when Ince's son Tom flicked home a low Stephen Crainey cross.
And the visitors went on to clinch the win late on when Gary MacKenzie bundled the ball in after Watford goalkeeper Jonathan Bond had spilled a corner.
The Blackpool boss said: "I thought it was a good game all round. When I look back on the whole game, I thought we were the better team.
"Watford came at us in the first 15 minutes, Jonathan Hogg should have scored for them with a header.
"We had a couple of chances and I wouldn't say we found it hard - but we took our time to get into the game.
"But once we got into the game I thought we looked a very, very good side."