The 23-year-old Slovakian, who missed the podium in downhill on Saturday, stormed to gold with his guide Martin Motyka.
The silver went to the oldest alpine skier at the Games, 55-year-old Mark Bathum of the U.S., who was just 0.13 seconds off Krako as he won his second career Paralympic medal. Canadian 16-year-old Mac Marcoux claimed bronze for the second event in a row.
The race used so-called "calculated time," in which each athlete's time is modified by a percentage reflecting the extent of their disability.
Over the nine days of competition in Sochi, a total of 72 gold medals will be awarded in five sports.