Wigan prop Flower became the first player to be sent off in a Grand Final when he twice punched New Zealand scrum-half Lance Hohaia in the second minute at Old Trafford to spark a mass brawl.
The Wales forward's inexcusable assault on Hohaia left last year's champions Wigan with a mountain to climb, but they were the better side in the first half and led 6-2 at half-time courtesy of teenage winger Joe Burgess' 20th try of the season just before the break.
Saints, already shorn of the influential Jonny Lomax, Jon Wilkin and Luke Walsh, appeared devoid of ideas in the absence of Hohaia but made their extra man count in the second half.
Sia Soliola marked his final appearance for the club with a try and Tommy Makinson's 27th try of the season made sure of victory as Saints ended their eight-year wait for a Super League title, having lost on their last five visits to Old Trafford.
Coach Nathan Brown will now return to Australia having guided Saints to the League Leaders' Shield and the Super League title, with James Roby picking up the Harry Sunderland Trophy for the man of the match.
Brave Wigan were left to reflect on what might have been had Flower kept his head.
Warriors coach Shaun Wane spoke of the "healthy hatred" between the two sides ahead of the game, but Flower took it too far when he saw the red mist with less than two minutes played.
The forward spilled the ball with the try line in sight and inexplicably took his frustration out on half-back Hohaia, knocking him to the deck with a punch and following that up with another sickening blow as the Saints man lay on the deck.
Referee Phil Bentham quite rightly gave Flower his marching orders and Hohaia followed him down the tunnel for treatment on a bloodied nose, but Saints were unable to take advantage of their numerical advantage in a disjointed first-half display.
Josh Charnley served a warning to Saints with an excellent run down the right flank and the reigning champions were in front with 19 minutes gone courtesy of a Matty Smith penalty.
The lively Smith slotted over against his former club after Adam Swift had been punished for obstruction.
Saints were short of ideas with ball in hand, but they were level just after the half-hour mark courtesy of a Mark Percival penalty after Blake Green had failed to release Roby.
Wigan continued to pose more of a threat going forward, though, and moved back in front on the stroke of half-time, when the clinical Burgess rounded off a slick move by going over in the corner.
Brown's men drew level eight minutes after the break, the powerful Soliola holding off three tackles to force his way over and Percival adding the extras to put them 8-6 up.
Saints were then indebted to an outstanding last-ditch tackle from Makinson to deny Liam Farrell, who looked set to score an outstanding individual try.
Smith spurned a chance to level the scores 16 minutes from time when he dragged a penalty wide of the far post.
And the prolific Makinson gave Saints breathing space with 11 minutes remaining as he took a high kick from Paul Wellens and powered his way over, leaving Percival to land a routine conversion.
There was no way back for Wigan as Wellens, equalling Jamie Peacock's record of 10 Grand Final appearances, finally got his hands on the trophy again.