Man-of-the-match Rory Fallon scored in each half as City failed to handle his tactics of dropping off to make space, something he deployed with devastating success.
It was a third home defeat for City who went into the West Country derby as Championship leaders and came out of it as they did in the game, clinging on to be second.
They pulled back a penalty from substitute Lee Trundle, after Jermaine Easter had handled charging a free-kick, but Fallon's strikes were decisive.
His first came from Gary Teale's corner right on half-time and they teamed up again just short of the hour to repeat the feat.
Facing a goalkeeping crisis Argyle made an emergency one-match signing, borrowing Rab Douglas from Leicester. He had nothing to do for the first half-hour, before beating away a fierce drive from Darren Byfield to get into the game.
He went on to make several decisive stops late on when Bristol invaded his area in search of an equaliser.
Byfield had been brought back to partner Dele Adebola in attack, but too often their raids broke down around the edge of the box, with a more fluid system Plymouth mopped up everything and were always looking to spring forward to put City under pressure.
Louis Carey, on his 500th game for City, was stretched to repel them but did so to claim top marks for his club.
Easter passed up a great scoring chance on the one occasion he got away from him and then the Hungarian Peter Halmosi worried the home side with two low shots.
The first rather miserably found the sidenetting, the second from 40 yards caught keeper Adriano Basso by surprise but he just managed to push it away.
Plymouth always looked the more likely to score and after Fallon's first goal City reacted by bringing on Ivan Sproule to give them more width.
The formula looked as though it might succeed when Marvin Elliott had two headers blocked, one of them on the line by Paul Wotton, but Fallon's second strike left City too much to do even with six minutes added in the second half.