The four-year-old son of American Pharoah succumbed to complications from emergency colic surgery that was conducted early last week.
A shattered Waller fondly remembered the gelding, who was bred and raced by Debbie Kepitis and family, who last season joined Dulcify, Mahogany and Hitotsu as the only horses to complete the Victoria Derby/ATC Derby double.
"This is a heartbreaking loss not only for the Kepitis family, but also for the entire team at Chris Waller Racing," Waller said.
"Riff Rocket will forever hold a special place in our hearts, remembered for the fighting spirit he displayed both on the racetrack and in his final days.
"Our thoughts go out to all those who had the privilege of working with and supporting Riff Rocket throughout his career.
"He will be deeply missed, but his legacy will continue to inspire us all."