A first-half double from James Ward-Prowse had put the Saints in the driving seat, but Andre Gray cut the deficit early in the second half and Doucoure got the leveller at the death, appearing to use his hand to do so.
It added to Mauricio Pellegrino's misery as his side's poor form continued, though Watford themselves have won just once over same period of Saints' top-flight winless run.
Having opened his account for the season in last weekend's FA Cup win over Fulham – setting up a fourth-round clash with the Hornets – Ward-Prowse picked up where he left off.
The midfielder broke the deadlock after 20 minutes as Southampton sought revenge for September's 2-0 loss to the same opponent at St Mary's Stadium.
Pellegrino's men continued to impose themselves on the game and, after Dusan Tadic and Wesley Hoedt had been thwarted by Heurelho Gomes, Ward-Prowse was on hand again to cap a swift counter-attack with a straightforward finish.
Watford fought back after the break, with Gray nodding in and Doucoure stealing the headlines in more ways than one, leaving the visitors to wish VAR was in use.