Wilson, who beat Judd Trump in the 2024 final in Belfast, made an emphatic start to the final in Belfast with a 101 break in the first frame to lay down an early marker.
Jones claimed the second, but Wilson won the next three frames with the help of breaks of 60 and 135.
The Welshman responded in style and registered a run of 130 in the sixth frame to at least keep himself in contention.
However, Wilson regained his control of the match and won the final two frames of the session to move to within three of victory.
The former world champion continued to dominate in the evening and kept his cool to win the opening three frames and lift the Alex Higgins Trophy.
Wilson won the Masters – arguably second only in prestige to the World Championship but a non-ranking event – at the start of the year.
His form since had been a mixed bag, so to land the Belfast title again and carry off the trophy memorialising Northern Ireland snooker great Higgins meant a lot.
“Obviously the trophy has got an absolute legend of our sport’s name on it in, so I am very grateful that I can take this trophy home for a second time,” Wilson said.
“I think the fans in Belfast quite like to see positive snooker. They like to see players going for their shots and maybe just trying to do something a little bit different every now and again when frames are over, and that’s what I’m all about.
“I’m about trying to entertain people and also trying to get the win at the same time, which is not an easy balance sometimes. I am very glad I managed to do that this week.”