There are flights from Bogota (BOG) to YYZ on AC. I doubt they are seasonal (they are operating now). I recently found this for someone who wanted to avoid going through the US to get from Colombia to Japan.

The only other way to get from Latin America to Japan if you want to avoid the US is Aeromexico and they are not in *A.

Both Avianca and Copa fly BOG to Havana. And Copa from Panama City but you obviously know that.