Lt. Norman Ogden and Lt. Donald Clark, both from Victoria, were on a training run at the time.
Retired Canadian Navy commander Al Horner, a friend of the pilots, says the weather was not good at the time, but the cause of the crash remains unknown.
"There's been lots of ideas floated around, but no, we don't know, " Horner told Stephen Quinn on The Early Edition.
"There wasn't enough of the bits and pieces of the airplane to be able to sort that out."
Today's ceremony included the unveiling for a stone cairn and plaque on Mt Strachan.
Surviving family members, as well as former Navy collegues like Horner, were in attendance.
Tragedy still raw for friend
Horner says until the memorial, he had not visited the crash site since November 1963, when he was involved in the search for his friends.
He says that, 51 years later, the tragedy still feels very raw.
It was compounded by the fact that, at the time of the crash, U.S. President John F. Kennedy had just been shot.
"We didn't realize that Kennedy had been shot until we landed on that afternoon. So it was a fairly intense start to the day," he says.
The search for wreckage took three days.
"It was very emotionally trying when we found the crash site," says Horner.
"There are some things that tend to stay with you. No matter how you bury them, they come out."
Whilst researching this story, the CBC found footage in its archives of the search for Lt. Norman Ogden and Lt. Donald Clark, dating back to Nov. 25, 1963.
The news item was never aired, because the report of the search was overshadowed by the fallout from the assassination of John F. Kennedy.
Here, you can watch that silent archive footage for the first time and below, read the script that was intended to accompany the pictures.
On mobile? Click here to watch the 1963 archive footage
On mobile? Click here to read the original 1963 script