Ricardo Fuller bagged his third goal of the season to win an eventful encounter at the rain sodden Britannia Stadium.
City fought back from 2-1 down to claim the victory and move up to fifth in the Coca-Cola Championship.
The Potters made it one-nil thanks to an own goal by Marcel Seip but the defender made amends for Argyle by equalising just after half-time.
The second own goal of the game saw Gabriel Zakuani put the ball into his own net following a mix-up on the line with Steve Simonsen before Liam Lawrence equalised and Fuller got the winner.
Boss Tony Pulis opted to replace Jon Parkin with Mamady Sidibe for the game and also made changes in the defence.
Zakuani and Clint Hill both returned to the City rearguard with the DR Congo international slotting in at centre half with Hill at left back.
The new look back line were tested right from the off as the visitors made a bright start to the game.
The Pilgrims could have took the lead as early as the first minute when Peter Halmosi struck the ball across goal from the left hand side but sadly for him his shot went two yards wide of Simonsen's post.
But it was to be the Potters who would get the early goal on eight minutes after a foul on Sidibe just outside the box.
A neat training ground free-kick routine involving Liam Lawrence, Rory Delap and Dominic Matteo saw the latter play the ball into the box for Sidibe.
He then found Richard Cresswell but his attempt on goal was blocked at the last moment with the ball trickling clear.
Lawrence was there though to pick the ball up on the right byline and stear it in the box where Marcel Seip headed into his own net to open the scoring.
Fuller had a chance to make it two-nil on fifteen minutes when Sidibe headed on Simonsen's goal-kick to play him through on goal.
The Jamaican held off the defender but after a little deliberation he could only fire straight at Plymouth keeper Luke McCormick.
His defence were all at sea though for the resulting corner, but they did manage to boot the ball away from danger when Sidibe and Lawrence were lurking following the initial poor clearance.
The visitors did remind City that they could still be a danger through David Norris on twenty minutes.
A neat turn and shot tested Simonsen but thankfully Norris' effort dropped over the bar.
Akos Buzsaky then went close from a free-kick following a foul on the Hungarian by Sidibe.
The midfielder struck a curling looping effort into the box from the left flank that nearly evaded Simonsen to drop into the top corner.
Simonsen was there to squash any danger of that happening but he nearly got caught out again when his mis-timed jump for a cross allowed the visitors to put an effort on goal.
Luckily, Ryan Shawcross was on hand though to head the ball over the bar for a corner and then head away the resulting cross.
Just before half-time, Peter Halmosi struck a powerful shot at goal that hit Gabriel Zakuani, but the deflection bounced away from danger and didn't drop into the net with Simonsen diving the opposite way.
Just after the break, Andy Wilkinson replaced Clint Hill following a rib injury he had picked up earlier in the game and it wasn't long until he was busy at the back with a Plymouth corner.
The flag-kick was whipped into the back post where Marcel Seip made amends for his earlier own goal to head the ball home and bring the visitors level.
Good football by Argyle continued and they should have really gone into the lead but Rory Fallon could only fire straight at Simonsen following good work on the left-hand side.
Fallon immediately went about making amends though and another effort on goal by the striker forced a mix-up and a collision between Simonsen and Zakuani on the goal-line, with the ball appearing to come off the defender on its way into the net.
Tony Pulis then chose to replace Richard Cresswell with Peter Sweeney as the Potters went in search of an equaliser.
And not long after, it came through Liam Lawrence.
A long throw from Rory Delap was flicked onto the back post where Lawrence appeared to place the ball home and send the crowd wild.
City continued to push for a winner and Sweeney played a great ball over the top of the defence for Ricardo Fuller.
His perfectly timed run beat the offside trap with the Jamaican going on to coolly lob the keeper and make it 3-2.
Fuller then had another chance with five minutes remaining after a ricochet put the striker through on goal.
McCormick was quick out of the Plymouth six yard-box though and closed down the striker to save his strike.
Sub Jon Parkin hit a speculative effort over the bar in the final moments but it didn't matter as the referee soon blew the whistle to confirm that all three points were the Potters.

CITY (4-4-2): Simonsen; Wright, Zakuani, Shawcross, Hill (Wilkinson 47); Lawrence, Delap, Matteo (c), Cresswell (Sweeney 63); Sidibe (Parkin 88), Fuller. Subs: Eustace, Hoult (GK).
PLYMOUTH (4-4-2): McCormick; Connolly, Seip, Timar, Sawyer (Hodges 88); Norris, Nalis (c), Buzsaky, Halmosi; Chadwick (Ebanks-Blake 69), Fallon (Hayles 69). Subs: Doumbe, Gosling.


















