The Hornets looked to be on course for only their second win in eight games when John Eustace volleyed them into a deserved first-half lead.
But Boro boss Gordon Strachan sent on Leroy Lita five minutes after the restart and the change reaped almost immediate rewards with the former Reading striker heading in the equaliser from close range just four minutes after entering the fray.
Crystal Palace's defeat against Cardiff City earlier in the day meant Watford went into their game knowing they would not end the day in the bottom three whatever the outcome.
But the draw means they extended their advantage over the third-from-bottom Eagles to four points going into this Tuesday's crucial showdown between the two clubs at Vicarage Road.
Watford almost went in front inside three minutes when keeper Brad Jones had to dive full-length to his right to keep out a 25-yard free-kick from Tom Cleverley.
Apart from a Gary O'Neil shot that went wide, the hosts were not particularly troubled defensively in the opening stages and in the 21st minute they took the lead.
Boro could only half-clear a corner to the edge of their area and the unmarked Eustace superbly guided a volley back through a packed goalmouth and past Brad Jones.
Full debutant Will Buckley and Cleverley had opportunities to extend the Hornets' lead, before Boro equalised nine minutes into the second half.
Lita started the move by winning the ball back in midfield and found O'Neil, but his deep cross to the back post looked to be over-hit.
However, Julio Arca hooked the ball back in at the far post, Scott Loach could only help the ball further across his goal-mouth and Lita was largely unchallenged as he nodded home.
But that was to be the only team the Watford defence was undone and they could have taken all three points when a Cleverley shot was deflected narrowly over and the unmarked Heidar Helguson failed to make a good contact from six yards out when another Cleverley ball was touched on by Danny Graham.