He had become the first person to successfully perform the difficult move in competition during his free skate at the US International Figure Skating Classic at Lake Placid, New York, last month where he won the gold medal.
Skating to "Euphoria" by Labrinth, he repeated the feat to thunderous applause during his free skate at his senior Grand Prix debut to take gold.
"I felt great," Malinin said. "I'm still in shock and I don't really know how I pulled that off. I just trusted in my practice and it worked out well. I knew when I stepped out on the ice for my warm-up that I would go for it.
"I made that decision and I didn't wander around and wonder if I should or not. I stuck with it."
Malinin had previously said that he was inspired by double Olympic champion Yuzuru Hanyu, who unsuccessfully attempted the quadruple axle during his free skate at the Beijing Olympics.
Japan's Kao Miura finished second behind Malinin and South Korea's Cha Jun-hwan took bronze.
Skate America is the first of six events in the International Skating Union Grand Prix of Figure Skating Series.