Dom Heaume put the hosts ahead inside three minutes before Ross Allen brilliantly smashed in the second to double the advantage.
Ben Gallichan twice hit the post for Jersey but despite having the bulk of possession they were not clinical enough in attack.
Karl Hinds pulled one back from close range but Guernsey held on for the win.
The result means the Greens have now won the title 46 times, Jersey 53, with one shared in 1937 and Alderney lifting the Vase once, in 1920.
Guernsey were quickest out of the blocks and went in front when Dave Rihoy's shot was palmed away by Jersey goalkeeper Euan van der Vliet, but Heaume was there to calmly volley in the rebound and give his side the best possible start.
At the other end Gallichan's angled header came back off the far post, before Allen's superb strike across van der Vliet from a tight angle flew in and put Guernsey firmly in control midway through the half.
Allen had latched onto a quickly taken Rihoy throw, catching the Jersey defence off guard, and has now netted in six different Muratti finals stretching back to 2010.
Gallichan fired against the post again after half an hour, when he should have hit the target but instead dragged his close-range shot onto the upright.
As the game wore on it was Jersey who dominated possession, with the Sarnians seemingly happy to drop deep and let their opponents have the ball in the middle third.
Striker Craig Russell, a surprise absentee from Martin Cassidy's starting line-up, was introduced from the bench on the hour mark as the visitors continued to have more of the possession.
It was fellow substitute Hinds who finally found a way past Leroi Riley, when the ball dropped to him in the box and his prodded effort found the corner of the net with quarter of an hour still to go.
The Reds went close through Jack Cannon's free-kick before the last golden chance for an equaliser fell to captain Cav Miley, but his strike from just inside the box went over the bar and Guernsey could celebrate only their second home Muratti triumph since 2001.
Guernsey got their hands back on the Murrati Vase with a hard-fought 2-1 win over rivals Jersey at Footes Lane.