The 26-year-old trailed Clara at the summit of the final climb as the Italian broke away however, as he tired towards the finishing line, the Frenchman found enough speed to win.
Manificat gained time on Clara down the hill and then made his move at the start of the final straight to win, after 30km combined in the skiathlon, by just 0.7 ahead of the Italian.
He has enjoyed a mixed start to the season having finished 44th in the 15km classic mass start last time out in Canmore and 14th in the stage event in Kuusamo before that.
However a third among the three races in Finland underlined his potential and he delivered it in the skiathlon in Canada for his second career win, the first coming back in March 2010.
Much like the women’s skiathlon, there was little between the top of the field as Norwegian Sjur Roethe claimed third a second behind Clara with Tobias Angerer just 0.2 further adrift.
Another Norwegian Eldar Roenning was 0.8 shy in fifth with Russia’s Andrey Larkov sixth, 0.2 behind, and Carla’s Italian teammate David Hofer 0.4 off in seventh.