On each occasion, McDonald denied the Lindsay Park team of Ben, Will and J D Hayes a feature Group 1 victory.
Sent out the $2.20 favourite, Riff Rocket scored a short-half-head win from Apulia ($4.20) with Sunsets ($13) a length away third.
McDonald said the Derby was a test of stamina with the three best horses drawing clear of their rivals in the run home.
"It would've been a great spectacle to watch but I've been blessed with a couple of really close photos and this is another one that I thought I was done to a dinner on the line," McDonald said.
"The poor Hayes boys, they will be hating on me.
"It's a real test for young horses.
"I was happy with the position because of his electric turn of foot, but I was cursing myself because he got there really quickly and was a sitting duck and I was lucky to get away with that one."
Riff Rocket showed a brilliant turn of foot to win the Listed Super Impose (1800m) at Flemington on October 7 before Sunsets had the better of the gelding in the Caulfield Classic (2000m) on October 21.
There were some questioning the stamina of Riff Rocket, but Waller was bullish all week about the three-year-old running out the trip.
Waller was in Sydney and assistant trainer Charlie Duckworth said the trainer was confident of success.
"We actually joked this morning with Chris that he was a bit confident ahead of today," Duckworth said.
"I don't know whether they should be playing Elton John's 'Rocket Man' or David Bowie's 'Space Oddity' if we were lucky enough to win but I don't think he'll care which song they play now."
Duckworth said horses need miles in their legs heading into the Derby.
"You'll see all of those horses, they've all at least had a run at two and it stands them in such good stead for their future preparations," Duckworth said.
"Even though we're looking after the horse and trying to give him as much time as possible, we try and get to a milestone with each preparation.
"Whether it be getting to a jump-out or to a trial or getting to a first race start without pushing the envelope too far.
"He's obviously done everything he's had to do to get to this point today."
What a finish!
