Warrington had led 6-2 in Manchester after an early try and conversion from Declan Patton, but Oliver Gildart cancelled out the first-half score in the 55th minute to leave the final delicately poised.
The decisive moment came in the 63rd minute when Josh Charnley, in his final Wigan appearance, crossed the line to ensure that the Riversiders repeated their 2013 final victory over League Leaders' Shield winners Wolves.
Shaun Wane's side had been beaten in the last two finals, but despite a host of late pressure from Warrington, never looked like surrendering the lead and it is now 61 years since Wolves have won a domestic title.
After scoring the decisive try, Charnley told Sky Sports News: "I told Shaun I'd like to go out with silverware. What a way to finish. I've been here many years, with these boys for years, it's going to be emotional but I'm looking forward to my next challenge."
Charnley will make the move to rugby union club Sale Sharks at the end of this season.