Having run away with the first match of the tie 27-9, Canada were in the driving seat heading into Saturday's match and despite a much-improved effort from the Eagles they were able to hold on for the victory.
The visitors came out firing and twice came within inches of scoring only to be held up by some resolute Canadian defence.
Eagles winger Takudzwa Ngwenya eventually opened the scoring with a five-pointer after Blaine Scully had done well to steal possession.
Canada responded soon after through a penalty from James Pritchard, and the full-back was on the board once more when he notched up the home side's first try after good work from a line-out just outside the USA 22.
Pritchard missed the conversion and with Chris Wyles adding a penalty for the USA, the teams went into the break tied at 8-8.
Neither side could add to their tally early in the second period and it wasn't until the 60th minute that the scorers were troubled once more.
Much to the delight of the home fans it was Canada who took the lead, with Jason Marshall sneaking over in the corner for a try. Pritchard again missed the conversion, but while the match was still alive, the tie was all but over.
Wyles kept his side in the match with a penalty but the Eagles lacked the penetration required to run in tries.
The outside centre had another chance to grab the victory in the dying moments with another penalty attempt, but he was wayward and Canada held on for the win.
The Canucks will take their place in Pool D of the World Cup where they'll be up against France, Ireland, Italy and the second qualifier from Europe.
The USA can still qualify for the showpiece event if they beat Uruguay next year in a two-leg contest for the final Americas berth.
For Canada: Tries: Pritchard, Marshall Penalties: Pritchard
For the USA: Tries: Ngwenya Penalties: Wyles (2)