The 29-year-old Russian was a contender for honours throughout the 50km in Norway and was part of a seven-strong leading pack with ten kilometres to go.
Seven became five with six kilometres remaining with Petter Northug one of the two to drop off with Roland Clara leading ahead of Legkov.
Clara, Legkov, Petter Eliassen, Martin Johnsrud Sundby and Ilia Chernousov remained together until the final metres when a decisive move split the field.
Legkov made the telling break and was not to be caught as he led into the home straight and took victory by 1.2seconds ahead of Sundby with Chernousov third another 0.7 adrift.
Eliassen and Clara couldn't keep up with those three and came home in fourth and fifth respectively while Northug battled to finish sixth 42 seconds behind Legkov in total.
World Cup leader prior to the 50km Dario Cologna trailed home over three minutes behind Legkov in 19th with the order of the overall standings changing as a result.
Legkov, who trailed Cologna by 107 and Northug by 84, now leads by 12 points ahead of the latter and three further ahead of the former with a total of 1233 points.
The Russian also holds the upper hand in the World Cup distance standings with a lead of 151 points ahead of defending champion Cologna.