Martin Allen tasted defeat in his first game in charge of Notts County as Yeovil consigned the Magpies to an eighth consecutive loss.
Magpies' Lee Hughes had a goal ruled off for handball before Dean Bowditch slid home a cross from Shaun MacDonald to give the hosts the lead.
John Spicer lashed home Ben Burgess' flick-on to make it 1-1.
But Bowditch beat keeper Stuart Nelson to the ball to poke home the winner just five minutes later.
Notts County, who Allen controversially took charge of this week after spending just 19 days with League Two outfit Barnet, slip one place to 22nd in the League One table, one point and one game behind Bristol Rovers and Walsall.
Any lingering fears Yeovil may have had regarding relegation should now be fully dispelled - they remain in 17th position but have moved seven points clear of the drop zone.
Yeovil Town manager Terry Skiverton told BBC Points West:
"I'm really pleased, not so much with the peformance, but we really needed to win this game.
"We've done it and got ourselves that much closer to safety, but we still want to kick on. Fifty one points and you can still go down, and our goal difference isn't very good, so there's still work to be done."
Notts County manager Martin Allen told BBC Radio Nottingham:
"I thought they done OK, they had a good go. The energy, effort and commitment from the players, the squad and the staff was good.
"They weren't weak, they had a go - but could've done with a bit of quality at times.
"We had some many chances in the first half to have gone ahead. The lads had a go but we have got to improve."