Irish Under-21 international captain Judge scored a 76th-minute penalty to secure the three points which lifted the home side a further place away from the bottom.
Judge's goal came within two minutes of a Scunthorpe equaliser, also from the penalty spot, by Gary Hooper.
That strike cancelled out the Pilgrims' opener, from New Zealand international striker Rory Fallon just before the hour mark.
Fallon, who now jets off to Bahrain for the first leg of the Kiwis' vital World Cup qualifying play-off next weekend, headed home Gary Sawyer's left-wing cross.
The 57th-minute goal was an exact replica of the one that had steered the Pilgrims to a first win of the season four days previously at Peterborough.
Fallon had come close to opening the scoring against Scunthorpe in similar fashion towards the end of an edgy first half, but stand-in goalkeeper Josh Lillis twisted well to tip the effort over his crossbar.
Scunthorpe will rue a slew of missed half-chances during that period as Argyle's young, inexperienced back four showed a lack of cohesion.
Hooper forced the Pilgrims' French goalkeeper Romain Larrieu into two fines saves and the Argyle number one also parried Cliff Byrne's close-range header.
Larrieu was at fault for the penalty from which Hooper levelled, when he came to claim a through ball that he should have left alone and ended up tangling with Martyn Woolford.
After Hooper converted, Argyle immediately won a penalty of their own when Judge was felled by Lillis as he chased captain Carl Fletcher's perceptive pass.
Judge recovered to slot the ball under Lillis and secure all three points for the Pilgrims.