Rooney headed home from a 32nd-minute corner to secure a 1-0 Betfred Cup final victory over Livingston at Hampden.
The Perth side held on without any scares to become the first club outside Celtic to win a major Scottish trophy since Hibernian triumphed in the 2016 Scottish Cup final.
The goal came from St Johnstone's first real opportunity and there were few others. Livingston had created a couple of half-chances to take the lead but could not carve out anything of note in response to Rooney's goal.
The wing-back scored in the two previous rounds and also in St Johnstone's recent league win over Livingston, which was the West Lothian's first defeat in David Martindale's first 15 games in charge.
Much of the media focus ahead of the final was on Martindale's incredible journey from a six-year prison sentence to a flying start to life in football management.
But opposite number Callum Davidson is also in his first season as a boss, having been assistant to Tommy Wright when Saints won the 2014 Scottish Cup.
The only down side for Saints came before the game when long-serving midfielder Murray Davidson failed to overcome a calf injury, having also missed the final through injury seven years ago.
Saints came into the final on form, having only lost to Celtic and Rangers in their previous 11 games, and fresh from a 3-0 win at Motherwell.
Manager Davidson made one change, leaving out striker Guy Melamed despite his Fir Park double. Wide player Craig Conway, who had impressed in the 3-0 semi-final win over Hibernian, came in.
Rooney overlapped early on and got a low cross which was deflected into goalkeeper Robby McCrorie's hands, but Livingston had the bulk of the early pressure from set-pieces and high balls into the box.
One of the latter fell kindly for Efe Ambrose, who volleyed well over from 14 yards, and another dropped for Josh Mullin, who produced a stylish strike from 20 yards which drew a one-handed stop from Zander Clark.
There was little football played in the opening half and Saints in particular struggled to get men forward.
But they made the most of their first corner in the 32nd minute. Rooney shrugged off the close attentions of Jon Guthrie to head Conway's outswinging delivery in off the post.
Livingston had a chance on the break but Nicky Devlin's pass was too strong to put Scott Robinson in on goal, and Rooney had a 30-yard strike saved before the interval.
Saints started the second half with the best piece of football of the game.
Conway's reverse pass sent Ali McCann to the bye-line and he cut it back for David Wotherspoon, whose first-time shot was stopped by McCrorie. Chris Kane could not readjust his body in time to force the rebound on target from close range.
The Perth side enjoyed a good spell of possession and Jamie McCart saw a header blocked by Ambrose after beating McCrorie to a corner.
Martindale brought on a succession of attacking substitutes after the hour mark. Craig Sibbald, Alan Forrest, Gavin Reilly and Jay Emmanuel-Thomas came on to join striker Robinson.
Livi forced more of the play into the opposition half but could not engineer a chance and Saints squandered some opportunities to hit their opponents on the break.