Perez now has three goals in five games for league-leading Dallas (6-1-1), which also benefited from an own goal by Vancouver's Brad Rusin to improve to 5-0-1 in its last six matches.
FC Dallas remained perfect at home, winning all five contests by a combined 9-2 margin.
The Whitecaps (2-2-3) dropped to 0-3-1 on the road this season and 0-3-2 in their last five matches overall.
FC Dallas, which has scored the opening goal in every game this season, went ahead 1-0 in the 29th minute on Rusin's own goal, then went up by two on Perez's goal in the 50th.
The Whitecaps began to apply more pressure after that, but Fernandez would not let anything past him. He preserved the shutout in the 88th minute when Tommy Heinemann raced in alone, but could only manage an off-speed chip shot that Fernandez calmly knocked aside.
Dallas controlled the action for most of the first 27 minutes, building a 6-1 edge in shot attempts, but Whitecaps goalkeeper Joe Cannon made several outstanding saves to keep the game scoreless, starting with a diving to deny Perez's 25-yard blast just 50 seconds into the contest.
He then managed to get a hand on Kenny Cooper's shot to deflect it just over the crossbar in the 11th minute and made a strong hand save on Perez's header in the 16h minute.
Dallas finally broke through when Rusin blocked David Ferreira's corner kick in the middle, but the ball bounced off him and landed just over the goal line before Cannon could clear it out.
The Whitecaps nearly tied it in the 41st minute when Fernandez couldn't hang on to Nigel Reo-Coker's 25-yard shot, leaving a loose rebound for Matt Watson that appeared headed in before defender George John made a sliding clear off the line.
Dallas players wore black armbands with the words "Peace" and "West" printed on them, honoring the casualties from this week's Boston Marathon bombings and the fertilizer plant explosion in West Texas.