Harvey's right ski broke early in the race and he was given a replacement from his team. With fog also coming down on the course, the native of St-Ferreol-les-Neiges, Que., covered the distance in nine minutes 3.4 seconds to edge Kershaw.
"It feels so good to be back on the podium after a slower start to the season," Harvey said. "My training has felt good, but I have not been able to confirm those good feelings during the races this year. To do that today is a huge relief for me and the entire program."
It's the second time that Harvey and Kershaw, form Sudbury, Ont., have shared the World Cup podium in cross-country skiing. The last time came in 2012 when Harvey and Kershaw finished one-three respectively in a prologue race at the World Cup final in Falun, Sweden.
While Harvey captured two of the four podium finishes for the Canadian squad last year, Kershaw has been shut out of the medals since Falun.
"This is huge today," said Kershaw. "After a difficult season last year, and a vicious start this year, this came as a big surprise today. I'm still pretty shocked."
Chris Jespersen of Norway was third, 10.2 seconds behind.
Ivan Babikov of Canmore, Alta., was 26th at 9:28.2.
In the women's prologue, overall cross-country World Cup leader Marit Bjoergen led a 1-2 Norwegian finish in a three-kilometre race.
Mild and rainy weather forced organizers to shorten the course and change the format of the competition, a decision that led to the withdrawal of four-time women's Tour winner Justyna Kowalczyk of Poland. The Olympic champion said it was unfair to have five freestyle and only two classical races in the seven-stage event.
"The changed program doesn't fit into my Olympic preparations," said Kowalczyk, a classical style specialist.
Bjoergen covered the distance in six minutes, 34.4 seconds to leave teammate Astrid Uhrenholdt Jacobsen 1.9 seconds behind. Sylwia Jaskowiec of Poland was seven seconds behind in third.
Denise Herrmann of Germany was fourth, ahead of Jessica Diggins of the United states.
Daria Gaiazova, of Banff, Alta., was the top Canadian, finishing 37th (7:01.3). Perianne Jones, of Almonte, Alta., placed 47th (7:03.2).
The Tour ends in Italy on Jan. 5.
— With files from The Canadian Press