Saints ran out 14-6 winners, with Wigan down to 12 men from very early on after Wales international Flower, 26, made unwanted history when he became the first player to be sent off in a grand final.
The incident came less than three minutes into a spectacle watched by a 70,102 crowd at Old Trafford.
Flower appeared to take exception to stand-off Lance Hohaia's use of a forearm on him during a Wigan attack and reacted by knocking him to the ground with a left hook.
The former Crusaders forward then struck his defenceless opponent with a second punch to the face while he laid motionless on the turf.
St Helens struggled for a long time to make their numerical advantage tell but second-rower Sia Soliola's try, on his final appearance in Super League, helped put his side in front for the first time after 53 minutes.
Winger Tom Makinson added a second 12 minutes from the end to clinch the club's first title for eight years.
Flower was banned for six months while Hohaia retired from rugby league the following April aged 32 because of "recurrent post-match concussion-type symptoms".