Watford bossed the first half but Troy Deeney saw his penalty saved by Matt Gilks, while Marco Faraoni struck the frame of the goal twice.
But Blackpool were much improved after the break and Ince's fine finish at the end of a mazy 81st-minute run made it four wins out of five for Paul Ince's men.
After Ricardo Fuller's header from a Barry Ferguson corner kick drew a diving save from Manuel Almunia in the second minute, the first half was one-way traffic as the visitors seized control of proceedings.
Minutes later, Deeney's rising 25-yard drive stung the palms of Gilks, before the striker was gifted a golden opportunity to open the scoring from the penalty spot after 12 minutes.
Neal Bishop hauled down Almen Abdi, but Gilks pulled off a wonderful diving save low to his left to deny Deeney and keep the game at 0-0.
Bishop, operating out of position at right-back, then failed to clear an Abdi free-kick and he was fortunate Gilks was again alert to tip wide Gabriele Angella's close-range effort.
Blackpool's injury-ravaged side were struggling to get out of their own half, with Watford dominating possession and laying siege to the Seasiders' goal.
Faraoni struck the woodwork twice towards the end of the opening period - his first effort a downward header that came back of the post, with Gilks pulling off an outstanding reaction stop from the follow-up, and his second an 18-yard curler that found the angle of bar and post.
For all Watford's first-half dominance, Blackpool came out for the second a rejuvenated side. Fuller's shot down the left-hand side of the box was tipped wide by Almunia after 48 minutes and Tom Barkhuizen - the hero last week - bundled a long throw-in from Ferguson narrowly wide.
Ferguson was at the heart of the home side's resurgence as he picked out the head of Kirk Broadfoot twice from corner kicks, but the centre-back could only head wide on both occasions, before Fuller blazed over on the volley from another raking long throw-in from the midfielder.
With Blackpool firmly in the ascendancy, Ince threw on son Tom and the introduction of the winger, who was far from match fit, proved to be the deciding roll of the dice.
Ferguson saw a free-kick tipped over the crossbar by Almunia after 77 minutes and moments later the home side took the lead courtesy of a wonderful solo effort from Ince.
The 21-year-old gathered possession midway inside the Watford half and waltzed past three defenders before rifling a brilliant finish into the bottom left-hand corner to give his side all three points.
Source: PA