Winnipeg's Brittany Schussler, Ottawa's Ivanie Blondin and Regina's Kali Christ posted a six-lap time of three minutes 2.81 seconds, missing out on a bronze medal by 0.77 seconds.
The Netherlands won the event in 2:58.19, ahead of Poland and South Korea.
Canada's roster for the team pursuit at the Sochi Olympics in February will be decided after the speed-skating trials in Calgary in late December and early January.
Christine Nesbitt, from London, Ont., is usually the fourth skater for the Canadian women's team pursuit. However, the 2010 Olympic 1,000-metre champion was not in Berlin this week.
The Canadian women were fifth at the 2010 Winter Olympics in Vancouver and won silver in 2006 in Turin, Italy. Canada's men secured a spot in the pursuit event on Saturday.
Individually, Heather Richardson led a 1-2 for the United States for her third win from four races in the women's 1,000. Richardson finished in 1:14.51 to beat compatriot Brittany Bowe by 0.91 seconds, with Russia's Olga Fatkulina 0.98 off the pace in third.
Calgary's Kaylin Irvine recorded her first World Cup top 10 with a 1:16.07.
That improves on her previous top World Cup finish, 12th in Astana, Kazakhstan seven days earlier on Dec. 1.
"I felt like things I've been working on in practice finally came to together for a whole race today." Irvine said. "I'm very happy with it."
Regina's Marsha Hudey was 16th in women's B 1,000 metres. It was Hudey's first World Cup race at that distance after six starts in the 500 metres in her first international season.
In men's competition, Olympic champion Mo Tae-bum of South Korea edged Japan's Joji Kato by two thousandths of a second to win the 500-metre event for the first time this season.
Mo, who won the 1,000 on Saturday, clocked 34.876 seconds to deny Kato what would have been his second win of the season. Dutchman Michel Mulder was third, in 34.95, in the final World Cup before the Olympic Games in Sochi.
William Dutton of Humboldt, Sask., placed 20th in the A 500 metres.
Dutchman Jorrit Bergsma defeated compatriot Jan Blokhuijsen for his first win of the season in the men's 5,000.
Overall leader Sven Kramer of the Netherlands didn't race and Bergsma took full advantage by clocking 6:14.82 to beat Blokhuijsen by 0.84 seconds.
South Korea's Lee Seung-hoon was third in 6:16.12.
Toronto's Jordan Belchos finished 10th in the men's B 5,000 metre, followed by Mathieu Giroux of Pointe-aux-Trembles, Que., 18th, and Regina's Lucas Makowsky was 20th.