Rory Fallon put Plymouth ahead in the 57th minute before the game revolved on two penalty's.
Romain Larrieu conceded a penalty that was converted by Gary Hooper in the 75th minute but immediately Argyle went down the other end and Alan Judge was felled by the Scunny keeper. Judge became executioner and slotted home for the winner.
Argyle have a couple of weeks off because of the international break and next face Ian Holloway's Blackpool and Bloomfield Rd on Saturday October 17th.