Ryan Taylor, on his first outing since August, had swept the Pilgrims ahead on 16 minutes before Tom James rose above Yann Songo’o to equalise in the second half.
Fellow home substitute Sam Surridge volleyed in a brilliant winner late on to set up a second round encounter with AFC Wimbledon at Huish Park.
Swansea City loanee Keston Davies was granted his first start since the opening day of the League Two season as manager Darren Way made five alterations to the side that lost at Wycombe Wanderers.
Bevis Mugabi, fresh from his three-match suspension, began at right-back, while Jake Gray, Alefe Santos and Connor Smith took up places in midfield.
In an uneventful beginning to the contest, Town pressed well and looked to zip the ball round with purpose; Argyle, however, were more direct with Omar Sowunmi and Davies winning the majority of aerial battles against experienced forward Taylor.
The ex-Bristol City man would get the better of the hosts’ backline just past the quarter of an hour mark with the game’s first shot and goal.
Aaron Taylor-Sinclair bombed down the left and across the byeline before cutting back to Taylor whose effort squirmed through the grasp of Artur Krysiak and into the back of the net.
Despite going behind, Yeovil’s intention to keep the ball on the deck remained but it was a lofted cross from Ryan Dickson that almost produced a clearcut chance for the green and whites.
Santos, at the base of a three-man middle, sprayed a delightful pass to the onrushing left-back who delivered towards the space Gray was surging into, but good defending from Sonny Bradley denied the 21-year-old an opportunity on goal.
As well as their objective to advance in numbers, it left spaces for Plymouth to counter in and bar the outstretched leg of Sowunmi to thwart Alex Fletcher’s close range attempt, it would have been 2-0 to the visitors.
Soon after, Jordan Green showcased his electric pace to steam past Gary Miller and his cutback was met by the swinging left foot of Olufela Olomola, though goalkeeper Mannion – the Pilgrims second emergency loan signing and sixth stopper of the campaign – was equal to it with a smart claim.
Town reverted to a 4-4-2 formation at the break, making two half-time substitutions. One of which was Otis Khan.
The winger went close with a curling effort before slaloming his way down the right and setting up Davies to strike, and he was rebuffed by a decent block.
Francois Zoko should have equalised prior to the hour. Santos showed good vision to pick out the Ivorian’s run in behind and when he lifted the ball over Mannion, he turned to celebrate but saw his cheeky lob drift marginally wide.
Two minutes later, Yeovil were deservedly level and it was the two changes that made it so.
Khan’s wicked set piece from the left was glanced home by James at the near post – the Welshman’s first ever professional goal.
Glovers front two Zoko and Olomola both had penalty appeals turned with the former lashing over in vain and Khan’s free kick hitting the side netting in a quiet final 30 minutes.
However, Town did have one more moment in front of goal which Surridge dispatched with aplomb.
The AFC Bournemouth youngster kept his eye on the ball to stroke home Olomola’s pinpoint delivery and complete an impressive turnaround.
Yeovil Town: Krysiak, Mugabi (James 46), Sowunmi, Davies, Dickson, Gray (Khan 46), Santos, C.Smith, Green, Olomola, Zoko (Surridge 83).
Not used: Maddison, Nelson, N.Smith, Bailey.
Plymouth Argyle: Mannion, Miller (Wylde 80), Edwards, Songo’o, Bradley, Taylor-Sinclair, Sarcevic, Carey, Threlkeld, Taylor (Ainsworth 72), Fletcher (Jervis 62).
Bookings: Bradley 48.
Not used: Childs, Grant, Sokolik, Diagouraga.