Ebanks-Blake pounced in the 22nd minute and Andy Keogh and Sam Vokes were also on target as Wolves ended a worrying run of five league games without a win.
Watford had arrived at Molineux on the back of confidence boosting wins in the FA Cup and Championship, but a failure to convert the chances that came their way proved costly as their relegation problems increased.
Adrian Mariappa did pull a goal back for Watford nine minutes from time but by then the damage had already done.
Crucially, Watford had been denied by two smart saves from Wayne Hennessey on the stroke of half-time which ultimately proved to be their undoing.
Ebanks-Blake's opener initially owed everything to the determination of Kevin Foley, whose surging run and cross forced a corner.
Kyel Reid then sent over a cross that Richard Stearman headed goalwards before Ebanks-Blake forced the ball home from six yards for the 50th league goal of his career.
Falling behind sparked Watford into life and they were unfortunate not to be on level terms just two minutes later when Will Hoskins was harshly adjudged to have fouled Hennessey when converting a cross from Tommy Smith.
Tamas Priskin was then denied by Hennessey before Wolves made a determined bid to double their advantage.
Keogh saw his shot cleared off the line by Lloyd Doyley before a smart save by Scott Loach frustrated Stearman.
Despite generally holding the edge, Wolves were still fortunate to take a lead into the second half.
On the stroke of half-time, it needed two wonder saves from Hennessey to keep Watford at bay.
First the Wales international saved at close range from Hoskins before seconds later tipping a rising 20-yard drive from Jack Cork over the bar.
Hennessey's heroics effectively signalled the beginning of the end of Watford's challenge and that was confirmed when Keogh struck for the fourth time this season in the 67th minute.
Ebanks-Blake won a tussle with Mike Williamson in midfield and fed Michael Kightly, whose right-wing cross was converted from 12 yards by Keogh.
But to their credit, Watford did not go down without a fight and grabbed hold of a lifeline nine minutes from time when Grzegorz Rasiak turned a Jobi McAnuff cross into the path of Mariappa who pounced at the far post.
But their hopes of a dramatic escape were ended once and for all in stoppage time when Matt Jarvis crossed for fellow substitute Vokes to power home a close range header.