Ellen White scored in the 92nd minute in what was a rematch of the 2013 Cyprus Cup final, also a 1-0 England victory.
Canada's Diana Matheson made her 150th appearance while newcomer Kylla Sjoman made her international debut.
"We are still trying some new things, so it may take us awhile to gel, but we are lucky because we have two to three years before we play in that FIFA Women's World Cup in Canada," said Canadian head coach John Herdman. "It is nice to be able to test a few things at this stage."
The Canadians next face the United States in a friendly June 2 at Toronto's BMO Field, a game that marks the team's homecoming following its bronze-medal performance at the 2012 London Olympics.