City’s Lee Peacock returned from injury to end the Pilgrims' eight-match unbeaten run.
In front of a West Country derby crowd of nearly 14,000, Peacock's eighth goal of the season midway through the first-half gave City their first league win at Home Park for 36 years.
Just for good measure, Peacock also cleared one of Argyle's best chances off the line. But the home side will count themselves unlucky not to have emerged with at least a point.
Former Bristol Rovers forward Micky Evans had a header cleared from the line, while Tony Capaldi hit the post, and substitutes David Norris and Blair Sturrock had decent efforts well saved by Steve Phillips.
The Pilgrims were also denied a late chance to equalise when Devonian Craig Woodman appeared to handle the ball in the penalty area, but referee Paul Armstrong waved away heated appeals.
The game's kick-off was delayed by 15 minutes because fans were caught in heavy traffic on the M5 and A38, but Peacock made the tortuous journey worth it for Bristol fans in the 27th minute.
Aaron Brown cut inside an isolated David Worrell on the City left and crossed to the far post, where Peacock was lurking to steer the ball home through goalkeeper Luke McCormick's legs.
Plymouth Argyle: McCormick; Worrell, Wottton, Coughlan, Gilbert (Hodges 81); Norris, Adams, Bent Capaldi Sturrock 72); Evans, Keith (Stonebridge 72).
Subs not used: Beresford, Aljofree.
Yellow: Evans
City: Phillips; Woodman, Butler, Hill, Bell (Fortune 57); Wilkshire, Burnell, Tinnion, A Brown; Peacock (Lita 75), Miller.
Subs not used: Stowell, Hulbert, Roberts.
Yellow: Butler, Lita
Att: 13, 923
Referee: P Armstrong