The scrum-half will quit the club for Hull later this month - but he made sure he left his last home game with a hero's exit.
Sporting a bizarre pineapple-like hairstyle, Long slowly squeezed the life out of a gutsy Wigan side.
He romped in for a try just before the break and, early in the second half, set up Francis Meli for his second try and a lead Saints never lost.
Wigan made it nervy at the end when Pat Richards went over and they nearly struck again with three minutes left, only for Long to pull off a try-saving tackle on Joel Tomkins.
Saints coach Mick Potter admitted his side had been forced to tackle ferociously to earn the win.
He said: "Sean was very good defensively - but he has certainly got plenty of practice.
"It was a really good performance against a very determined team and we soaked up a lot of pressure in the second half. There were some real special things done to stop them scoring. You could sense both teams were desperate to win to go to the next stage. It could have gone either way. We are just fortunate that we are there and we are happy to be so."
Wigan boss Brian Noble is another big name leaving at the end of the season, but unlike Long he will have no Old Trafford finale.
He is expected to travel to Wales to take over at the Celtic Crusaders.
He said: "I've known I'll be leaving for a week now. I sat down with chairman Ian Lenagan and we decided perhaps a change is for the best, and that's the way it's going to be. But it's not about me - it's about the players tonight. I thought they were awesome.
"It could have gone either way. I am absolutely thrilled for the players for the way they played but absolutely gutted for the way they went out of this competition.
"It was a fabulous game and we played some fantastic stuff in the second half. The players have been wonderful all year."
It was heartbreaking for a Wigan team who have now missed out on Old Trafford at the final hurdle for the third year running.
Saints have lost to Leeds in the last two finals and have been out of form recently - but this display bodes well for next Saturday.
Kyle Eastmond beat three Wigan tacklers to put in hairy wing Meli for the first try.
But Saints had to rely on a series of bone-crushing, try-saving tackles by Long to keep the Warriors out.
Wigan did score when Sam Tomkins struck with a killer high kick. Pat Richards and Saints winger Ade Gardner were both fooled by the wind and the bounce fell kindly for George Carmont to race in.
Richards added the conversion for a 6-4 lead and the Warriors hung on to superbly until shortly before half-time, when Long raced in to put the Saints ahead.
Meli increased the lead but the Warriors refused to give up and Richards gave them hope with a late try.
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