The Frenchman had stooped to meet Troy Deeney's headed pass but appeared to use his hand to divert the ball past Southampton goalkeeper Alex McCarthy.
James Ward-Prowse had earlier struck twice in the first half, in the 20th and 44th minutes, as Southampton looked set to end their dismal nine-match winless streak.
Yet lacklustre Watford brought on their totem Deeney at halftime and roused themselves after the break, Andre Gray heading home in the 58th minute before the late drama surrounding the home side's equaliser.
In the week that VAR was trialled in English football in FA Cup and League Cup ties, Doucoure's goal looked set to reignite the debate about the need for the technology to be used in the league to prevent similar incidents.
Southampton manager Mauricio Pellegrino was dismayed by what he felt was an "injustice."
"I am sad," the Argentine told the BBC. "I never see this type of mistake in the Premier League before. To live this injustice is really hard.
"I think we have to try (VAR) and analyse if it's possible to help the sport to make better decisions, even for the referee."
Before the Southampton protests, Doucoure had appeared to take a quick look at the assistant referee to check that the goal had stood before wheeling away to celebrate.
"They'll feel like it's a loss. VAR comes in we probably wouldn't get that but today we got it. It's the luck of the draw," Deeney told Sky Sports.
(Reporting by Ian Chadband, editing by Pritha Sarkar)
Share
