The 11-year-old was ridden home by Timmy Murphy to become the first horse since Androma in 1985 to win the contest twice, having previously won in 2010 and also finishing runner-up last year.
Auroras Encore led at the last but Merigo powered ahead to cross the line first ahead of the Ryan Mania ride.
King Fontaine finished third, 15 lengths off the winning pace.
Murphy said of his winner afterwards: "He's a superstar. Andrew knows him better than anybody and I think he just comes to himself at this time of year.
"The choke was out for a long way and all credit to how deep he dug for me. I couldn't go any quicker and his jumping was keeping him it. He's a great horse to own and ride."