The Premier League outfit found themselves a goal behind with a little over 10 minutes on the clock, after Ikechi Anya brought down an opponent inside the box.
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Neither side could really create any clear-cut chances as the first half continued, with Adebayo Akinfenwa heading over his side's best opening since their early spot kick.
Watford did manage to draw level prior to the interval in the most fortunate of circumstances, however, with Odion Ighalo seeing a clearance from the goalkeeper come back off his back and loop into the net.
Fernando Forestieri was denied an instant second by some good goalkeeping, ensuring that it remained all square at the break.
A fully-changed Wimbledon side emerged for the second 45 minutes, but it was Quique Sanchez Flores's charges who found the game's third goal through Forestieri's bundled close-range finish.
New recruit Jose Holebas was given a 15-minute run-out at the end of the pre-season affair, but it was an afternoon that ended in relative disappointment for the visitors as Francomb converted from the spot after Andy Barcham was felled inside the box.