Watford lost their place at the top of the Championship after David Norris's 89th-minute winner earned Plymouth three vital points at Vicarage Road.
Norris gave the visitors the three points when he turned in Barry Hayles's excellent cross from the right.
Watford had created good goalscoring chances but Damien Francis and Tommy Smith were both denied by the woodwork.
Plymouth's Krisztian Timar had the ball in the net but was denied when he was adjudged to have fouled Richard Lee.
Watford boss Aidy Boothroyd:
"Teams come here and try to stifle us.
"We had enough chances to win and we also had enough warnings they could take something from the game, which they did at the very end.
"I think the priority for us is to win at home. We've got some things to put right as this was not acceptable."
Plymouth boss Paul Sturrock:
"We came with a game plan and stuck to it well.
"The boys stuck to the game plan that we have been working on the last few days and it's nice when something from the training ground comes off.
"We made it very difficult for them and stifled their creative players. It showed the character that is imprinted in the squad."
Watford: Lee, Doyley, Jackson, DeMerit, Stewart (Mariappa 72), Smith, O'Toole, Williamson, Ainsworth (Francis 46), King, Priskin (Ellington 65).
Subs Not Used: Loach, Shittu.
Plymouth: Larrieu, Sawyer, Timar, Seip, Hodges, Gosling, Norris, Abdou, Halmosi, Hayles, Easter.
Subs Not Used: McCormick, Doumbe, Ebanks-Blake, Chadwick, Summerfield.
Goals: Norris 89.
Ref: Darren Deadman (Cambridgeshire).