Fernandez broke a scoreless tie in the 52nd minute when he got under a Mauro Rosales corner kick in the middle of the area and sent a header past Colorado goalkeeper Matt Pickens.
Johnson doubled the advantage 11 minutes later. Rosales again provided an assist, launching a left-wing cross that the Seattle striker headed home.
The Sounders (8-5-6) snapped a nine-game winless streak, the longest in club history.
Omar Cummings scored for the Rapids (7-10-1), who fell for the fourth time in five games.