Riff Rocket joined Raveneaux (1987) and Mahogany (1994) as the only previous three-year-olds to have won the Debonair Stakes/C S Hayes Stakes and Victoria Derby double.
Mahogany went on to capture the Group 1 Australian Guineas (1600m), a race Riff Rocket will head to in two weeks' time.
Ridden by Craig Williams, Riff Rocket ($7) scored a three-quarter length win from King Colorado ($4) with Verdad ($7.50) the same margin away third.
Riff Rocket again showed his liking for the open Flemington track where he has now raced four times, registering three wins.
Waller's assistant trainer Charlie Duckworth was down from Sydney for Saturday's meeting and suggested Riff Rocket was likely to be kept to shorter trips than the 2400m of the Group 1 Australian Derby at Randwick in April.
"I know he won a Derby, but we genuinely believe he didn't stay out the distance that well," Duckworth said.
"I was told he is the first horse in 30 years to win a Derby and come back and win this race, so full credit to the horse.
"He's a real trier and we had three riders in the race, and I think they all wanted to potentially ride this one.
"Whatever he's been doing in his trials, all the right form judges were on him, and I think we'll enjoy the win.
"It was a lot less stressful than the Derby."
Duckworth said the Australian Guineas was where he and Waller thought Riff Rocket would be primed to show his best.
So, he was a little surprised with the return victory over 1400m.
"The plan was to stay here for the Australian Guineas in a fortnight and we thought that realistically that is where we thought he'd be at his prime," Duckworth said.
"But to show how sharp he was today is fantastic so I'd image the plan won't change too much but hopefully he can get a picket fence together."
