It is the ninth time Saints have lifted the famous trophy, and came in comprehensive fashion against their greatest rivals.
Scrum half Sean Long inspired the win and earned the Lance Todd Trophy as Man of the Match with a fine all-round display and six goals, while centre Willie Talau scored two tries.
The afternoon got off to a wonderful start for Saints, who opened the scoring inside three minutes.
The chance came after Kris Radlinski was unable to get his kick away under pressure from Jason Hooper, with Talau collecting and putting Lee Gilmour in from 25 yards.
Long converted to open up a 6-0 gap, but Wigan came back strongly.
Firstly, Andy Farrell saw a try ruled out by the video referee for a knock on after losing the ball in Paul Sculthorpe's attempted tackle.
The Warriors managed to level matters on 13 minutes, Farrell, Gareth Hock and Radlinski combining to free Adrian Lam down the middle.
The Papua New Guinean was obstructed after chipping over Paul Wellens, but Terry Newton raced through to scoop up the ball and score under the posts, Farrell levelling matters.
Kevin Brown was also denied a try - following an earlier knock on - as Wigan pressed, but it was Saints who broke the deadlock with a Long penalty after Quentin Pongia caught Wellens high.
Long turned creator for Saints' second try, on 23 minutes, with a deft grubber kick which Willie Talau collected above Dave Hodgson to touch down, the conversion creating a 14-6 lead.
Danny Orr's last-gasp tackle saw Darren Albert put a foot in touch to be denied a score soon afterwards, while Saints' substitute winger Dom Feaunati was placed on report for a high tackle on Kevin Brown.
Wigan used the field position gained by that penalty - and a knock on from Martin Gleeson - to cut the gap to four points, Lam putting Brett Dallas in at the corner.
But Sants provided a killed touch on the stroke of half time, keeping the ball alive for Keith Mason to allow Wellens to score at the side of the posts.
Albert was again denied at the corner early in the second half, this time by a wonderful cover tackle from Radlinski, but there was little the full back could do on 50 minutes to prevent a crucial score.
Brown collected a loose ball inside his own quarter but then attempted to offload, gifting possession to Paul Sculthorpe, who was tackled but then supported Long to power to the line.
Long converted and added another penalty to open up a commanding 28-10 lead, with Pongia going on report for the high tackle on Mark Edmondson.
Saints went close to extending their lead, firstly when Long's kick just bounced dead ahead of Talau and then when Hodgson tracked back to stop Edmondson after a Long break.
Wigan gave themselves hope on 67 minutes, with Brown surging clear from inside his own half before putting Dallas in for his second, Farrell's goal cutting the lead to 28-16.
But Long ensured the win two minutes later, chipping over and collecting his own kick before allowing Gilmour to send Talau in.
It was a fine try, and ensured that Saints would end their superb Challenge Cup campaign victoriously.
St Helens coach Ian Millward admitted that winning the Powergen Challenge Cup on Saturday was one of his greatest triumphs.
Saints capped a brilliant Challenge Cup campaign with a 32-16 win over Wigan Warriors at The Millennium Stadium.
They defeated last year's Finalists - Bradford and Leeds - as well as Hull and Huddersfield on their way to Cardiff, and Millward was delighted that his side finished the job in style.
"It feels fantastic," said Millward. "We've been lucky enough to win a lot of trophies while I've been here, but I think it gets better every time.
"Our preparation was absolutely outstanding - it couldn't have gone any better.
"We had a tough time last year, on and off the field, and the guys have got stronger every week.
"I've got a bunch of guys here were are very honest, committed to each other and very keen to get improve their game.
"We've had a really tough draw, but that didn't give us the right to win the game, all it did was give us the right to compete in the game, and we competed very well.
"Overall, it was a fantastic team effort.
"Our body language was good and, just before half time, it looked like we were getting a little stronger.
"The secret for us was how we started the second half, doing the little things right."
The win gave Saints captain, and second half try scorer, Paul Sculthorpe his first trophy since taking over the role at the start of the season.
"It's unbelievable," he said. "To lead the boys up there and pick up the trophy is an amazing feeling.
"If we'd got here and lost, nobody would have remembered the games we won. It means nothing if you don't pick this up, but we have come here and turned Wigan over in the Final.
"Out of the top six (of Super League at present), we have beaten five of them and we are the other.
"It's an amazing feeling, but it's also a credit to the squad. To miss out is hard for some of the guys - (broken ankle victim) Mick Higham has been as much of an influence as anybody in getting us here.
"It's a squad effort and we'll all celebrate together."
Warriors coach Mike Gregory had no complaints after the game.
"I'm very proud of the effort," he said. "In the second half it went away from us and our inability to complete with the best attacking team in the competition killed us.
"Our players had a dig and certainly tried to play, but I've no arguments, the best team won.
"We couldn't control their offloads on a number of sets, and we've got to learn and be stronger in coliision."
Saints scrum half Sean Long was named as the Lance Todd Trophy winner as Man of the Match, after playing a starring role for the victors.
"Sean was excellent," conceded Gregory. "He deserves the Lance Todd Trophy - he kicked us to death."Like