Troy Deeney had given the Hornets a first-minute advantage with his second goal of the season, although he received a helping hand from Boro defender Andre Bikey.
The Cameroonian defender sent an intended back pass straight into the path of Deeney, who beat England Under-21 stopper Jason Steele at the second attempt.
The direction of the match changed in a costly 10-minute spell for Boro as Emnes firstly equalised with a clever finish on the half-hour mark.
Watford striker Matej Vydra was then dismissed just before the break for an alleged stamp on Boro midfielder Nicky Bailey.
The visitors capitalised on their numerical advantage in the second period as McDonald, who was making his first Boro appearance since April, found the bottom corner from 18 yards to earn his side their second away win of the campaign.