Minutes earlier, Switzerland's Marianne Fatton also made history as she beat big favourite Emily Harrop of France to become the first Olympic champion in the sport that is making its Games debut in Bormio.
After coming through heats and a semi-final in a relentless snowstorm, Cordona Coll dominated his final, making no mistake through the various transitions to beat Russian Nikita Filippov with France's Thibault Anselmet taking the bronze.
Spain's only previous Winter Olympics gold was won by Alpine skier Francisco Fernandez Ochoa at the Sapporo Games in 1972.
Filippov was competing as a neutral athlete without a flag or anthem after the IOC banned Russian and Belarusian athletes from the Olympics following Moscow's invasion of Ukraine in February 2022.
Harrop, a four-time SkiMo overall champion, was the overwhelming favourite to win gold in Bormio.
But she lost time after the stairs section of the course and could do nothing to catch Fatton, taking silver.
Ana Alonso Rodriguez's bronze was Spain's first medal of the Games but compatriot Cardona Coll went two places better with a commanding race to gold.