Tony Pulis got revenue over the Baggies in his first game facing his former club since he was dismissed in November 2017.
In typical Pulis fashion, his Middlesborough side scored in the last minute from a long free kick into the Albion area.
Craig Dawson jumped under the ball and Ahmed Hegazi ran into Kyle Bartley allowing Daniel Ayala to fire past Sam Johnson.
Despite scoring 7 in their previous game, Albion struggled to create any clear chances against Pulis' well drilled Boro side.
"It's a sickener to lose it in the final few minutes of the game," Baggies boss Darren Moore admitted. "We just lost the flight of the ball in the air - I think if we contest it we come away with a clean sheet.
"You've got to give Middlesbrough credit, they changed their shape to combat us. They went with a defensive display and they'll probably feel they got it right in terms of nullifying us.
"It's a disappointing one to take because I thought during the 90 minutes we played the game right."