He finished ahead of American Daniel Powers and Venezuela's Juan Mendez.
The native of Humboldt, Sask., was a favourite to win the wakeboarding competition and did not disappoint.
Malinoski was clearly relaxed on the water, pumping his fist and egging on the crowd to cheer louder in his final pass.
He finished with a score of 89.11.
Earlier, Whitney McClintock of Cambridge, Ont., won gold in the women's water skiing event.