Paul Wotton's late penalty gave Plymouth all three points as George Burley's stuttering start as Southampton boss continued in the Coca-Cola Championship.
Wotton struck eight minutes from time after Claus Lundekvam handled in the box.
Earlier, Nick Chadwick's opener for the home side had been cancelled out by young midfielder Andrew Surman's first ever goal for the Saints.
The game started 15 minutes late due to a power failure at Home Park, and the delay seemed to affect the players in a disappointing first half.
Burley made just one change to the side which beat Leicester in the FA Cup on Saturday, with Surman coming in for the injured David Prutton.
Argyle made one change from their winning side of seven days ago - also against Leicester - with Hungarian midfielder Akos Buzsaky returning to the side in place of the suspended Tony Capaldi.
The home side were quickly on the front foot with Lilian Nalis' header testing Bartosz Bialkowski in the Saints goal.
Bialkowski and his opposite number Romain Larrieu were tested at set pieces, but it was not until Nathan Dyer's 20th-minute effort - comfortably saved by Larrieu - that there was another real effort at goal.
The game struggled to get going as both sides gave plenty of free-kicks, and the stop-start nature of the encounter was typified by the lack of clear-cut openings for either side.
Micky Evans had a chance to score the first goal six minutes before half-time, but fired over from 12 yards.
However, the Pilgrims did finally make the breakthrough on the stroke of half-time when Chadwick volleyed home a left-footed effort from 12 yards out after a poor defensive clearance from Claus Lundekvam.
Burley made a change at the break, replacing the ineffective Marian Pahars with Kenwyne Jones, but it was Plymouth who had the second half's first chance with Buzsaky's shot was kept out by Bialkowski.
Dexter Blackstock then headed wide from Surman's free-kick, before Darren Potter headed over from a Surman corner and the lively Surman himself then had a shot blocked by Anthony Barness.
The breakthrough finally came for the visitors - and Surman - after 69 minutes when the youngster headed home Chris Baird's right wing cross.
Four minutes later, Jones had a chance to give the Saints the lead, but Larrieu was able to catch his effort.
And the Saints were made to pay in the 83rd minute when Wotton stepped up to drill his ninth goal of the season - and his fourth in the last three games - high into the centre of Bialkowski's goal.
Plymouth Larrieu, Barness, Doumbe, Ward,Aljofree (Connolly 57), Norris, Wotton, Nalis,Buzsaky (Djordjic 79), Evans, Chadwick.
Subs Not Used: Hodges, McCormick, Zebroski.
Booked: Aljofree.
Goals: Chadwick 45, Wotton 84 pen.
Southampton Bialkowski, Baird, Lundekvam, Higginbotham,Brennan (Kenton 47), Dyer, Oakley, Potter, Surman,Pahars (Jones 45), Blackstock.
Subs Not Used: Smith, Fuller, Cranie.
Booked: Pahars, Kenton.
Goals: Surman 70.
Att: 15,936
Ref: A Hall (W Midlands).