Fernandez took a pass from Pedro Morales and launched a shot about 30 yards out that sailed past goalkeeper Stefan Frei. It was Vancouver's first goal since June 7, ending a two-game scoring drought.
Major League Soccer-leading Seattle dropped to 11-3-3 with the loss that snapped its winning streak at three games. Vancouver improved to 6-3-7.
The Whitecaps pressed for most of the first half and created several good scoring chances.
In the 19th minute, Morales lofted a free kick from a sharp angle that landed in the box. The ball sat tantalizing for a few seconds, but was cleared before a Whitecap could touch it.
One of the prettiest plays came in the 33rd minute when defender Steven Beitashour sent a perfect cross to a charging Erik Hurtado, but the forward sent the shot high and wide.
In extra time of the first half, Morales struck a curling shot that Frei stopped.
Seattle's best scoring chance in the first half came in the 19th minute when a header floated over top of the Whitecaps' net.
The Sounders began to press in the second half. Midfielder Lamar Neagle came close in the 52nd minute, firing a shot that drifted just wide of the Vancouver net.
Seattle's Tristan Bowen, a second-half substitution, fired a shot in the 60th minute that took a dangerous bounce before being gobbled up by goalkeeper David Ousted.
Seattle midfielders Osvaldo Alonso and Gonzalo Pineda sat out because an accumulation of yellow cards.