Nesbitt, from London, Ont., finished in one minute 15.48 seconds at Thialf Oval. She edged out Hong Zhang of China. Laurine van Riessen of the Netherlands was third.
Kali Christ of Regina was 14th.
It was Richardson's second World Cup title, after also winning in 2011. The 23-year-old from West Valley, Utah, won four of the seven 1,000 races this season.
Richardson's teammate, Brittany Bowe, was fourth to give her second place in the season standings. Karolina Erbanova of the Czech Republic was third overall and Nesbitt was fourth.
Dutch sprinter Kjeld Nuis was third in the men's 1,000 behind countrymen Stefan Groothuis and Mark Tuitert, but it was enough to seal the season World Cup title.
Groothuis finished in 1:08.91 to lead the Dutch sweep of the podium. American skater Shani Davis' fourth-place finish was enough to take him to second in the season standings, leapfrogging Hein Otterspeer, whose disappointing 10th-place result dropped him to third for the season.
Tyler Derraugh of Winnipeg was eighth.
Nuis did not win a single race in the World Cup 1,000 season, but his consistency earned him top spot.
Another Dutch skater, Ireen Wust, had the performance of the day in winning the 3,000 race in a blistering 3:58.68, becoming the first woman to break the four-minute mark at Thialf.
She led another Dutch 1-2-3, with Diane Valkenburg second and Linda de Vries third. Cindy Klassen of Winnipeg was 13th.
Martina Sablikova of the Czech Republic won the season title ahead of German veteran Claudia Pechstein and Valkenburg after finishing in sixth place on Saturday.
In another race dominated by home country skaters, Olympic champion Sven Kramer fell just short of breaking his own track record as he won the 5,000 in 6:10.78.
Jorrit Bergsma was second in 6:15.74 to ensure he won the season title, in part because Kramer did not compete in two World Cup races. Bob de Jong was third in Saturday's race to take second place in the overall standings, just ahead of Kramer.
Jordan Belchos of Toronto was 15th.
With files from The Associated Press.