Along with the prestigious Paul Hunter Trophy, the victory earns Murphy a cool £350,000 as he finished off the match with a tremendous century break.
Wilson mounted a remarkable comeback in the evening session after trailing 6-2 at the interval, winning five of the first seven frames with impressive breaks of 95, 78, and 65 to narrow the deficit to just one frame at 8-7.
However, Murphy held his nerve at the critical points, particularly after Wilson missed a long red to the right corner in the 16th frame, allowing Murphy to compile a valuable 55 and move within a frame of victory.
Murphy ultimately sealed the deal with his fourth century of the match, ending a 10-year drought in Triple Crown events.
"I can't believe it - I'm in shock," a jubilant Murphy told the BBC.
"If I'm totally honest I thought these days were gone.
"When I lost to Mark Selby in 202 at the Crucible, I thought my days in the business end of these events had gone.
"But everyone knows I've teamed up with Peter Ebdon and he's helped me rediscover that self-belief, he's helped remind me I used to be quite good at this.
"There's still a bit of life in the old dog yet.
"I must pay tribute to Kyren - he is a great world champion. He really took it to me and there was a stage a few frames ago when it was panic stations."
Wilson said after the loss that he did not put up enough of a fight against the eventual winner.
"I just made it too easy for Shaun today," Wilson told the BBC.
"I threw him in the balls too many times and you can't do that with how well Shaun's been playing this week.
"I proved why I'm the world champion, I fought as hard as I could. From 8-4 down, a lot of people would have written me off and if the red goes in at 8-7, that could have been my clearance for 8-8 and you might be looking at the different scoreline.
"But every credit to Shaun - well done to Shaun."
Shaun Murphy took a commanding 6-2 lead over world champion Kyren Wilson in the opening session earlier in the afternoon.
In-form Murphy, who secured a 147 maximum break in his semi-final victory over Mark Allen, dominated the early stages.
A break of 94 in the opening frame set the tone, and he extended his lead to 3-1 at the mid-session interval.
Wilson, who was beaten by Allen in the 2018 final, struggled to find his rhythm as he sought out his first career Masters crown.
He briefly rallied, winning the sixth frame with a half-century break to narrow the gap to 4-2.
However, Murphy quickly regained control, compiling back-to-back century breaks to establish a strong advantage heading into the concluding session on Sunday evening.