The silver performance came a day after Harvey won gold in the men's 30-kilometre race.
Harvey racked up six medals this season (three gold, two silver and one bronze) en route to finishing third in the overall World Cup medal count.
Harvey's previous best in the overall standings was sixth in 2012 — the same year Devon Kershaw had the best overall finish ever by a Canadian male in second place.
"I'm super stoked. That was a super nice way to end the season," said Harvey. My skis were awesome again today. The wax techs did an awesome job. I'm so happy.
"I had kind of given up on the overall when I had to pull out of the final stage of the Tour de Ski because so many points are given in that race, but I was able to gain a lot in the last weekend," said Harvey.
Harvey, from St-Ferreol-les-Neiges, Que., started the pursuit with a 26 second lead on the field based on time over the first two races this weekend — a fourth place finish in the sprint, and his third victory of the season in Saturday's skiathlon. The top-two athletes skiers in the field, Norway's Martin Johnsrud Sundby and Russia's Alexander Legkov, worked together to hunt down the 25-year-old Harvey for a second straight battle to the wire.
Sundby ended up finishing first in 34 minutes 48.1 seconds. Harvey clocked-in at 34:53.0 for the silver medal, while Legkov won bronze for the second straight day with a time of 34:59.1. Legkov also secured second in the overall standings.
"I started at my own pace, but didn't want to go into the red zone. I knew the guys were coming, and they came back to me at the six-kilometre mark. Then it became tactical," said Harvey.
Kershaw of Sudbury, Ont., saved two of his best races of the season. The 31-year-old had solid back-to-back 12th-place finishes. Kershaw finished Sunday's race at 37:34.1.
Ivan Babikov, of Canmore, Alta., rounded out the trio of Canadian men in 23rd place at 40:05.9.
Andrea Dupont, of Timmins, Ont., was the lone Canadian woman in the women's 10-kilometre pursuit race. Dupont placed 42nd at 28:38.4.
The Norwegian women swept the podium. Therese Johaug locked up the overall World Cup title with a victory, finishing in 24:25.5. Marit Bjoergen was second at 25:54.7, while Heidi Weng skied to the bronze medal at 26:17.9.