David Flitcroft's first away game as Bury manager ended in defeat as Plymouth moved six points clear of the League Two relegation zone.
Caolan Lavery put the home side in front with a shot from inside the box after meeting a pass by Luke Young.
Bury levelled with Chris Sedgwick's chip over Luke McCormick after Daniel Nardiello hit a post for the Shakers.
Reuben Reid then completed the scoring with a close-range shot following an assist from Lewis Alessandra.
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Plymouth boss John Sheridan told BBC Radio Devon:
"It was a good goal from Caolan [Lavery], I'm pleased for him. He's done well to direct his shot and put it in the back of the net, and it was a great finish.
"When you score the first goal it gives you something to hang onto and you've got a better chance of going on to win the game.
"Unfortunately I thought we came out a little bit too slowly in the second half and their goal looked too easy. It was a good finish from the lad, but it was too easy passing the ball around in front of us and it gave them the incentive to push on.
"Reuben [Reid] was going to come off immediately before the goal - things just didn't go his way today. But I'm pleased as he ends up scoring the winning goal. He was in the right place in between the posts."
Bury manager David Flitcroft told BBC Radio Manchester:
"It's not going to be a quick fix. It's going to get a lot worse before it gets better.
"Two years of doing the wrong things are not going to be fixed in two games. I've got two years to turn it around and I'm looking forward to doing that, but it's definitely going to take time.
"I know where we're going to be at the end of the season - we'll be in League Two. There are a lot of hard games coming up but we're certainly prepared for a fight."
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