Canada, which took the first game of the two-match series against the United States 51-7, erased the Americans' 10-point lead to complete the sweep with a 48-point edge on aggregate.
"It wasn't a great performance, but we found a way to win," said Canada coach Francois Ratier. "But we always say good teams find a way to win so maybe we are a good team."
Trailing 10-0 at halftime, Ratier made substitutes that resulted in his team bringing more speed.
Canada's Elissa Alarie finished off an impressive push on the line that was sparked by a Laura Russell run that brought the ball deep into the Eagles' end.
Alarie's try, which went unconverted, gave Canada an 11-10 lead.
A penalty kick by second half substitute Andrea Burk in the dying minutes sealed the win for Canada.
Burk, who was influential from the moment she came on the pitch in the second half, was named the player of the series.
"When Burk came in and started to put all the back line in the right direction, things happened," said Ratier. "Once we started to go forward, it made a difference. That's the first principle of rugby."
Magali Harvey was Canada's other point-scorer as she converted two of her three penalty kick attempts. The fullback got Canada on the board early in the second half as she knocked it through the uprights from 22 metres out. After a yellow card was issued to the U.S.'s Kate Daley for unsporting behaviour midway through the second half, Harvey punched her penalty kick through from 40 metres out.
The Americans got first half tries from Amanda Street and Sharon Blaney. Neither tries were converted.
Saturday's match capped a two-week selection camp in Langford as Canada prepares to compete at the 2014 World Cup in France in August.