Jamie Gregg of Edmonton was second in 34.96 and Ronal Mulder was third in 35.04 at the Thialf oval.
The Canadian women`s pursuit team also took silver, finishing second in 3:03.50. South Korea took the gold and Poland earned bronze.
The result gave South Korea the season victory over archrival Canada, which was equal on points going into the race.
The Canadian pursuit team includes Kali Christ of Regina, Christine Nesbitt of London, Ont., Brittany Schussler of Winnipeg and Ivanie Blondin of Ottawa. Christ, Nesbitt and Schussler raced in the final.
With one final 500 race Sunday, Dutchman Smeekens can no longer be caught by Joji Kato of Japan, who is second in the season rankings.
"I surprise myself sometimes," Smeekens said. "34.8 here in Thialf, five victories in a row and the first Dutchman ever to win a 500-meter World Cup title. It's a milestone."
Smeekens won six of the last seven races this season to run away with the title.
Germany's Jenny Wolf won the women's 500, as Olympic champion Lee Sang-hwa of South Korea suffered her first defeat over the distance in this World Cup season.
Wolf's first 500 win of the season left her with a remote chance of beating Lee to the overall title with one race to go Sunday.
Wolf won in 37.77 Friday, ahead of China's Wang Beixing and Lee.
The Dutch fans had more to cheer about as the Netherlands won both the men's and women's team pursuit races in the final events of the evening to capture the overall World Cup titles.
The men, led by Olympic 5,000-meter champion Sven Kramer, won in 3:40.64 seconds to complete an unblemished season in which they won all four pursuit races.
South Korea finished just over two seconds behind the Dutch team and just ahead of Russia in third.
With files from The Canadian Press.