The Irishman, who will turn 87 next month, had high hopes for the son of Dawn Approach as he tussled with favourite Sir Dragonet inside the final furlong.
However, it was Aidan O’Brien’s charge – one of seven in the race for the Ballydoyle handler – that came through to land the year’s fourth Classic at Epsom.
In a tight finish, Madhmoon was only half a length down on the winner but in turn just a nose ahead of third-place Japan.
Broome was a short-head back in fourth while Sir Dragonet also finished a short head adrift in fifth.
Prendergast’s charge had every chance but the man who first took out a trainer’s licence in 1963 was far from downbeat after the contest.
‘We’d loved to have won, but we’re very proud of the horse,’ he said.
‘(My heart) always pumps, but that made it pump a little bit more.
He ran great, we’re happy with him.
‘It was a very good ride from Chris Hayes and he did nothing wrong.
The best horse won on the day.’
All systems go for another National bid.
Setback suffered in Clonmel victory.
Another gutsy display at Huntingdon.
Seven jockeys were given 10-day suspensions.
Hilly Way triumph for one-time Arkle fancy.