Irishman Culloty said he went through the "worst few minutes of my life" before it was confirmed, after a some 10-minute delay, that the result would stand after the 20-1 surprise winner had prevailed - a short head in front of On His Own (16-1).
In a dramatic finish, just inches separated the front two, along with third-placed The Giant Bolster (14-1), as the trio battled it out side by side up the testing uphill finish at Cheltenham.
Lord Windermere, who had appeared to have been out of contention for a large part of the race, had drifted right after the final fence and stewards looked at whether the winner, ridden by Davy Russell, had caused interference to the runner-up and third finisher.
"On balance we did not think the minor interference had cost the second the race," said stewards' secretary Paul Barton.
"If we have any doubt, the doubt goes to the horse in front."
Culloty, who won three successive Gold Cups on Best Mate for trainer Henrietta Knight between 2002 and 2004, said he "almost expected to lose the race".
"I'm in a total state of disbelief to be honest," he said.
"I couldn't believe it during the race and then when the stewards was announced, I thought we were certain to lose it given my luck."
Winning connections may yet face a battle to keep the race after Willie Mullins, trainer of On His Own, said he would consider an appeal.
"I'll have a chat with the owner and see what he wants to do, talk to (jockey) David (Casey) and see what he thinks and talk to people that know a little more than I do as the appeal will be in England and I need to see what the chances are of us getting a result," Mullins said.
"It's a nice prize to win but it is not necessarily the way you want to do it. We'll see what happens."
Casey, a late replacement as jockey after Ruby Walsh and Paul Townend suffered injuries in the first race, said he would have won had he not been "impeded".
"I felt that, with a straight run, I would have won the race. I got interfered with a couple a times... I felt all the way up the straight I was being impeded."
Culloty, who retired from the saddle in 2005 after a succession of injuries, followed in the footsteps of Fred Winter, Pat Taaffe and Jonjo O'Neill in becoming the fourth man to both ride and train the winner of the Gold Cup.
"Halfway round I was going to sack the jockey. He's not moved a muscle and he's come from nowhere," he said.
Russell, who enjoyed a day to remember with three winners, added: "I'm obviously delighted and relieved. It was nerve-wracking. I knew I was under no pressure and I just took a chance of going down the inside and he's done it.
"I was on the best horse in the race. Throughout the race I probably wasn't in the best position from where Jim wanted me to be.
"I couldn't ride a winner for Jim all year but he kept saying 'wait for Cheltenham, wait for Cheltenham' and how right he was."
Victory was particularly sweet for Russell who at the end of last year lost his job as top jockey to Ryanair boss Michael O'Leary's Gigginstown Stud in Ireland.
O'Leary was out of luck in the Gold Cup on Friday after Last Instalment, whose trainer Philip Fenton faces a number of charges in Ireland in relation to possessing unlicensed substances, including anabolic steroids, fell in the latter stages.
Last year's winner Bobs Worth, sent off the 6-4 favourite, finished fifth.
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