The 26-year-old scored his fourth goal of the season less than 10 minutes after coming off the bench to cancel out Kike’s 49th-minute strike.
Watford then pressed for a winner and Joel Ekstrand hit the post with a header as the Londoners finished strongly but had to settle for a 1-1 result.
But after dominating the first half and the opening part of the second, manager Aitor Karanka’s home side were full value for the point after creating a string of chances.
Watford’s first problem of the afternoon came before kick-off when goalkeeper Heurelho Gomes pulled up in the warm-up and had to be replaced by England Under-21 international Jonathan Bond.
Bond was the busier of the two goalkeepers on show in the first half.
Middlesbrough went close in the 13th minute after good work by Albert Adomah on the left. His cross was laid off nicely by Kike but Patrick Bamford’s rocket was blocked by Daniel Tozser.
Bamford should have put Middlesbrough ahead in the 24th minute when George Friend’s cross found him, but Bond managed to stick out a leg to deny the on-loan Chelsea striker.
Watford forced a fine save from Dimi Konstantopoulos when Matej Vydra’s low shot was tipped wide by the Greek goalkeeper.
Konstantopoulos showed good reflexes again when Watford winger Ikechi Anya found space on the left side of the box and hit a powerful angled cross which the goalkeeper palmed away.
Middlesbrough took the lead in the fourth minute of the second half, when after great work by Adam Clayton and Ryan Fredericks down the right, Bamford pulled the ball back for Kike who lashed the ball past Bond for his fifth league goal of the season.
Bamford almost doubled the lead a minute later when he ghosted into the box with some clever footwork before he was denied twice.
But Watford drew level on the hour when Deeney, who had replaced Fernando Forestieri less than 10 minutes earlier, smashed Anya’s cross past Konstantopoulos.
The goal gave the visitors confidence and they started to get on top.
Only the woodwork stopped them from taking the lead in the 69th minute when Ekstrand’s flicked header from Tozser’s ball hit the post.
Middlesbrough, up against it, found an outlet in Fredericks down the right and his cross to the far post found Kike but he shot back across the face of goal trickled wide.
The game was there for the taking as it opened up in the last 15 minutes, with both sides looking for a winner.
Tozser’s long-range free-kick was tipped wide by Konstantopoulos as Watford pressured the home side. Middlesbrough had a late surge but they had to settle for a share of the points.