The hosts dominated possession throughout the first half, but were forced to wait until the 39th minute for the clearest opportunity to open the scoring as Victor Bernardez brought down Watson inside the box.
The one-sided nature of the contest continued into the second half, with Sebastian Fernandez firing just wide of the target from a tight angle.
It came as little surprise to see Vancouver extend their lead when Morales turned provider by delivering a corner onto the head of Watson, who powered the ball home from close range.
Busch was forced to make a number of saves to ensure San Jose were not embarrassed by a heavier defeat, with both Morales and Fernandez being denied by the veteran shot-stopper.
There would be no late response from the Earthquakes, who remain second from bottom in the Western Conference.