The home side took the lead in the second minute when Joao Plata picked up the ball just outside the area and drove into the box before placing a shot into the bottom corner.
Real doubled their advantage when Ned Grabavoy knocked the ball to Alvaro Saborio inside the penalty area and he curled an effort into the top corner with a left-footed strike.
After the break, Salt Lake came close to getting their third of the game as Javier Morales crossed to the near post for Saborio, but his header hit the underside of the bar, bounced on the line and was hacked cleared.
Vancouver were handed a lifeline late in the game when Darren Mattocks's shot wasn't held by Rimando, and Niclolas Mezquida reacted quickest and fired the ball into the net.
The Whitecaps got their equaliser in stoppage time as Fernandez fired home from 30 yards with a strike into the bottom corner to hand his side a point.