Fernandez opened the scoring in the 12th minute - unleashing from distance - and it proved to be the match-winner at BC Place Stadium in Vancouver.
The Uruguay striker received a pass from Whitecaps team-mate Pedro Morales and the 24-year-old fired a 30-yard strike past Sounders goalkeeper Stefan Frei.
The Whitecaps had chances to double their advantage, while the Sounders had opportunities of their own but it was the Vancouver outfit that emerged triumphant on home soil - ending Seattle's six-game unbeaten streak.
Seattle remain atop the standings in the West after 17 games, seven points clear of Real Salt Lake and 10 ahead of the fifth-placed Whitecaps, who have a game in hand.
Elsewhere on Sunday, DC United moved top of the Eastern Conference after overcoming Toronto 2-1 in an entertaining battle at BMO Field.
After a scoreless opening half, visiting DC United made the breakthrough courtesy Nick DeLeon in the 54th minute.
Toronto - boosted by the return of United States international midfielder Michael Bradley from FIFA World Cup duty - responded immediately, with former Premier League striker Luke Moore levelling proceedings six minutes later.
Ryan Nelsen's men were unable to build on the Englishman's goal and DC United made them pay through Perry Kitchen, who headed home a 70th-minute corner.
Toronto - winless in three games - are fourth in the standings on 21 points, having only played 14 matches.
As for DC United, they have collected 28 points and are three clear momentarily at the summit ahead of Sporting KC's clash against Chicago Fire on Sunday.
Meanwhile, a 94th-minute goal from Erick Torres handed lowly Chivas USA a much-needed 1-0 victory at home to the Montreal Impact.
After some neat build-up play, Torres - a Mexico youth international - reacted quickest inside the penalty area with a stunning bicycle kick in the fourth minute of injury-time.
Chivas are second-from bottom in the West on 20 points, though they have played two games more than the SJ Earthquakes (16 points).
Montreal's (14 points) defeat left them a point adrift of the Fire at the foot of the table in the East.
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