Micky Evans had put Plymouth ahead when he nodded in an Akos Buzsaky cross before Tony Capaldi squeezed in a left-footed shot.
Marlon King's 18-yard drive pulled one back for Watford only for Paul Wotton to match his strike and restore Plymouth's two-goal lead.
But Ashley Young emerged as Watford's hero when he curled in a free-kick and slotted in a shot to level.
"The manner in which we conceded goals against a team we were leading against is obviously worrying.
"It is disappointing that we conceded three goals at home and obviously we have got a lot of work to do before we play Derby at home on Saturday."
Watford boss Adrian Boothroyd:
"We turned up and we thought we'd just get a bit of Devon sunshine but it doesn't happen like that.
"I have never seen or been involved in, or watched a game where there is such a change in attitude to wanting to win.
"What was said at half-time remains private but the players responded to what I said in a very professional fashion and I am delighted."
Plymouth: Larrieu, Barness, Doumbe, Aljofree, Brevett, Norris, Wotton, Buzsaky, Capaldi (Djordjic 64), Evans, Chadwick (Taylor 60).
Subs Not Used: McCormick, Gudjonsson, Connolly.
Goals: Evans 4, Capaldi 12, Wotton 43.
Watford: Foster, Doyley (Stewart 39), DeMerit, Carlisle, Chambers, Young, Blizzard, Bangura (Mahon 45), McNamee (Devlin 51), King, Henderson.
Subs Not Used: Chamberlain, Bouazza.
Booked: Bangura, Foster, Devlin, Chambers.
Goals: King 35, Young 52, 61.
Ref: L Probert (Gloucestershire).