Shishkin got the better of their first meeting in the Clarence House Chase at Ascot, winning by a length and taking his unbeaten record over fences to seven.
But in a dramatic rematch, the Nicky Henderson-trained Shishkin never travelled with any fluency at the back of the pack and was pulled up by Nico de Boinville after jumping the sixth from home.
Energumene (5-2) was always travelling well, despite the very soft ground, and once Chacun Pour Soi had exited when going well toward the head of affairs at the fifth last, Paul Townend's job appeared much simpler.
Energumene, who had lost his unbeaten record at Ascot, had last year's winner Put The Kettle on in his sights and turning in, had beaten off the mare.
He picked off Envoi Allen and once setting sail two out, it was Funambule Sivola (40-1) who gave vain chase in second, although he was soon in Townend's rear-view mirror.
The eight-year-old went on to beat his six rivals by eight and a half lengths, with Envoi Allen a further four and a half lengths back in third.
Willie Mullins - winning the race for the first time - said: "We just thought we got the tactics completely wrong at Ascot so the plan today was to follow Shishkin.
"The problem Paul then had was you could see after two fences Shishkin wasn't handling the ground so it then became a case of when was Paul going to forget about Shishkin and ride the race. Nico was wise in pulling Shishkin up, you could clearly see he hated the ground.
"I was very disappointed to see Chacun Pour Soi go out of the race when he did. I was gutted for Patrick (Mullins) because he appeared to be loving it. He might have given him a race.
"At every stage, though, Energumene seemed to be cantering and these extreme conditions suit him.
"He probably has more speed than we thought, at Ascot we felt after the race we should have waited rather than make all.
"That was the only plan I could come up with to turn the tables on Shishkin.
"It was a bit of an anti-climax for the neutrals but it was more nerve-wracking for me because you could see he was travelling the whole way."
He added: "It's great to finally win it, it's great for Paul and great for Tony Bloom (owner). When the rain came he began to get very confident."
Townend said: "I was on a very good horse and you can make it look easy then. He'd won on very heavy ground in Ireland so that wasn't going to worry us.
"It didn't work in Ascot and the tactics kind of went out the window early on (here) as well, he was enjoying himself. I let him jump up there and just kept holding on to him."
Bloom, who is the owner of Brighton & Hove Albion football club, said: "I did believe, I believe in Willie and in Paul Townend, who rode a magnificent race. The rain really helped us, we were praying for rain and were all getting really wet, but we're delighted to be wet.
"He's an amazing horse and we were confident going in, he's won the Champion Chase and it's brilliant.
"We were very excited, four or five out we were getting very confident. Obviously Shishkin pulled up and that made it a lot easier for us, but full credit to Energumene. A brilliant horse, we're having a great time."
Of Shiskin's run, Henderson said: "He wasn't where he wanted to be and I knew why, he just couldn't get out of it (the ground).
"We're in very extreme ground, yes he's won on soft ground but you're going round in heavy ground.
"That is not his scene, obviously."
Henry de Bromhead said of Envoi Allen and Put The Kettle on: "I thought Envoi ran a cracker, I wouldn't have mind seeing him on better ground.
"His wind just catches him out, especially on that ground, but I thought he ran a blinder, he jumped really well.
"The mare (Put The Kettle On) was a little bit disappointing."