Replays showed that referee Phil Bentham had little choice but to send off the Wigan prop and things almost worsened for Shaun Wane's men when Matty Bowen knocked on metres from his own line. However, Saints were unable to breach the Warriors rearguard in the early minutes.
Wigan were able to keep their local rivals at bay for 17 minutes and took the lead after Louie McCarthy-Scarsbrook was penalised for obstruction, with Matty Smith striking the penalty between the sticks.
However, it was the Warriors who took a surprising lead at the interval when Joe Burgess touched down in the corner with the final attack of the half.
Saints continued to make handling errors, but finally got over the Wigan try line through Sia Soliola in the 54th minute, with Percival kicking the extras.
The Warriors did not give up after falling 8-6 behind and ought to have retaken the lead when they managed to stretch the St Helens defence, but, with Josh Charnley in space on the right wing, Bowen failed to deliver a pass and crucially knocked forward.
Smith then had a good chance to get Wigan back on terms midway through the second half, but his penalty was wide of the uprights.
Saints held on for victory to add the Super League trophy to their League Leaders' Shield and end a run of five straight defeats in the Old Trafford showpiece event.