Flixton skipper Will Norman won the toss and elected to bowl first again, Fillongley edging their way to 206-8 from their 40 overs.
Jamie Nesfield, Tom Norman and Harry Walmsley took two wickets apiece, with Jake Hatton and Richard Malthouse claiming one wicket each.
In reply, Flixton bounced back from the early loss of Stu Stocks for four and raced away to 150-2 from 21 overs, Tom Norman the next man to go for 47.
Opener Malthouse was next man to go, having made a superb 80, with the score on 150-3.
That was to be Fillongley's last moment of joy, as skipper Will Norman (26no) and youngster Will Hutchinson (24no) saw the visitors home.
Flixton will now play the final of the competition at Lord's on Sunday September 16.
Skipper Norman said: "It turned out to be comfortable. I was nervous, we lost two wickets in two balls.
"It feels awesome to get over the line.
"It's seven in a row where we have batted second, just because we are used to it.
"We bowled too many wides, but maybe that was the pressure of the semi-final on our young lads.
"It means everything (to get to the final), the club have got to two semi-finals before, so to get over the line and to a final is great.
"Thank you to all the fans who have come down, they've been brilliant.
"Thanks also to Fillongley for having us, it's been a good atmosphere."
Club secretary Dave Hutchinson added: "What a tremendous afternoon, from top to bottom.
"From chairman Mel Brown right down to committee members, tea ladies and everybody, it's fantastic.
"We fielded outstanding and deserved to win the game.
"We got off to a flyer going at 10 and over, lost two wickets, but big Will (Norman) and little Will (Hutchinson) got us over the line."
The final of the competition is on Sunday September 16.
DON'T MISS: More reaction from Flixton's victory in Thursday's Scarborough News.