Former Wednesday striker Steve MacLean bit the hand that once fed as his first half goal gave Plymouth all three points at Hillsborough.
MacLean, making his first start for the Pilgrims since the end of August, pounced midway through the opening period and condemned the Owls to three successive defeats.
Despite bossing possession for almost the whole of the game, Wednesday lacked the requisite edge in front of goal, allowing the Pilgrims to seal an undeserved smash and grab.
Brian Laws made one change from the side that went down 3-1 at league leaders Birmingham on Saturday. With Jimmy Smith kicking off a four-match suspension, the Owls boss brought Francis Jeffers back into the side and reverted to a traditional 4-4-2 formation.
Plymouth forged two quickfire corners early on, neither of which troubled Lee Grant between the Wednesday sticks. At the other end, Jeffers sent Steve Watson racing clear on goal with a clever ball but the club captain was denied at the last by Chris Barker.
The early throes continued at a steady pace on a freezing Hillsborough night as Jeffers lashed in a fierce drive deflected over the bar for a corner. Wednesday were forcing the pace with Etienne Esajas looking lively but it was Leon Clarke who came close to opening the scoring. The big striker sold his marker a clever dummy and Jeffers fed his partner the perfect pass but Clarke's shot whistled past the post.
Johnson tested Roman Larrieu a minute later and the Argyle keeper was equal to JJ's daisycutter. But for all Wednesday's pressure, it was the visitors that stole into the lead through MacLean on 23 minutes. Played onside by Johnson six yards out as the Owls defence appealed for a free kick, the Scot seized on a loose ball and turned to beat Grant with a prodded effort in front of the Kop.
The contest then slipped into a lull with neither side threatening until Clarke broke free down the left of the Plymouth penalty area before cutting a neat ball back that forced Barker into evasive action.
Sean McAllister had the ball in the net three minutes before half time but the goal was ruled out by referee Graham Laws for an earlier foul on Luke Summerfield by Clarke. So totally against the run of play, Plymouth entered the interval a goal to the good.
After a lacklustre start to the second half, Wednesday made a double substitution on the hour with Frank Simek - making his first appearance since last December - coming on for Richard Wood while Jeffers made way for Deon Burton.
Moments later, the Owls could have drawn level when Clarke was sent through on goal by Burton but Craig Cathcart came to the Pilgrims' rescue with a well-timed tackle just as the striker was about to pull the trigger.
As MacLean went off to a warm reception from all four sides of Hillsborough, current Wednesday crowd favourite Akpo Sodje was introduced by Laws. But despite adding a further threat in the final third, Sodje could not help the Owls fashion an equaliser and Plymouth - who beat the Owls at Home Park a little over three weeks ago - made the long haul back to the south coast with their first double of the season in place.
Owls: Grant, Buxton, Wood (Simek 57), Spurr, Gilbert, Johnson, McAllister, Watson, Esajas (Sodje 71), Jeffers (Burton 57), Clarke
Unused substitutes: Boden, Small
Plymouth: Larrieu, Duguid, Paterson (Timar 74), Clark, Barker, McNamee (Walton 62), Seip, Summerfield, Cathcart, MacLean (Fallon 68), Gallagher
Unused substitutes: Marin, Noone
