Jonjo O'Neill, who was secured his first Gold Cup as a trainer, said: "AP was brilliant on him, he knows him so well.
"Our big worry was keeping him in the race as, if he makes mistakes, he gets behind.
"A lot of work has gone into him at home so was a great team effort from the yard.
"He only came right in last 10 days or so and we weren't really confident.
"He flowered in the last few days and it was spot-on timing."
Tony McCoy, who secured his second Gold Cup victory after Mr Mulligan took the title in 1997, said: "He's an amazing horse and it was an amazing performance. I'm so pleased to win it for JP as he's been so good to me.
"Jonjo has done an incredible job. I've got a Grand National and a Gold Cup out of the man and I love him to bits."
Winning jocket Tony McCoy said: "It's great for Jonjo and JP McManus. He's really delivered today. He was off the bridle the whole way and when I missed the third-last I thought my chance had gone."
Dual winner Kauto Star was pulled up at the ninth fence by Ruby Walsh after losing his place.
Synchronised, trained by Jonjo ONeill and ridden by Tony McCoy, won the Betfred Cheltenham Gold Cup.