The former Manchester United trainee stabbed the ball home from six yards after Jay Bothroyd had headed a centre from Michael Gray across the face of goal.
It was rough on relegation threatened Wednesday, who had battled back from falling behind after just 11 minutes when Andy Keogh pounced with his third goal in two games.
Marcus Tudgay's fifth goal of the season only eight minutes later fired Wednesday back on to level terms and they should really have gone on to take control of the game before Ebanks-Blake's late heroics.
Leading scorer Akpo Sodje, who was later stretchered off with an ankle injury, wasted a one-on-one with goalkeeper Wayne Hennessey in the 59th minute and Richard Hinds headed over the bar when well placed 60 seconds later.
Wade Small was then denied by an 89th minute save by Hennessey paving the way for Ebanks-Blake to strike.
Wolves had dominated the first period but, not for the first time, lacked a clinical cutting edge in front of goal and that looked set to be costly before Ebanks-Blake came up with his second goal since arriving at Molineux.
Keogh should really have broken the deadlock after just two minutes as he smashed a shot from only six yards against the bar after a neat Matt Jarvis cross.
Small was equally wasteful for Wednesday four minutes later when he failed to hit the target after being picked out by Jermaine Johnson.
It proved to be a pivotal moment as Keogh was not to be denied when he was presented with a second chance.
The Irishman pounced after good work by Ebanks-Blake, seeing his shot from ten yards deflected home off Tommy Spurr.
But Wolves could not build on Keogh's opener and they were quickly pegged back following a mix-up between central defenders Rob Edwards and Darren Ward.
Edwards, a ninth minute replacement for the injured Neill Collins, tried to clear a Glenn Whelan cross but bundled it into Ward.
The ball bounced off Ward and into the path of the grateful Tudgay who drove home a low drive past Hennessey.