
Valencia started slowly with the much publicised threat from Juan Mata, David Villa and Joaquin Sanchez failing to fire and instead it was Valladolid who caused most danger down the wings through Pedro Leon and Jonathan Sesma.
But Fernandes scored the only goal of the game when he fired a powerful shot from the edge of the area after 54 minutes to put Valencia on top of the table on 16 points.
Villarreal also have 16 points after a 2-1 win on Saturday against rock-bottom Real Betis but are in second spot on goal difference.
Earlier Sunday, Sevilla bolstered their Champions League hopes for nest season with a 4-0 mauling of Athletic Bilbao to move into third place on 14 points.
The home side never allowed tiredness from their midweek UEFA Cup efforts effect them as they went ahead after 26 minutes through Frederic Kanoute and then five minutes before the interval Renato Santos doubled their advantage.
The best goal of the game came after 75 minutes in a well-worked counter-attack with Adriano Correia providing the finishing touch. Substitute Ernesto Chevanton wrapped up the game with ten minutes to go.
"It's going well but it's still early days. We maintained a good rhythm and that is what we need to continue doing until the end of the season but it will be long and hard," said Manolo Jimenez, who has set a record by becoming the first Sevilla coach to string together eleven matches without defeat.
Barcelona are in fourth spot on 13 points after their 6-1 thrashing of Atletico Madrid on Saturday.
Sporting Gijon moved off the bottom of the table with a surprise 2-0 victory over Real Mallorca with goals from Carmelo Gonzalez and Roberto Canella.
They were the first points for Sporting against a side unbeaten in four matches, but after surviving some early scares their counter-attacks cut through Mallorca and they could have had more with Mate Bilic hitting the post.
Pierre Webo missed from the penalty spot for Mallorca.
Malaga made easy work of struggling Recreativo Huelva as they beat their Andalusian neighbours 4-0.
Eliseu Pereira dos Santos scored the first of his brace in the first minute of the game and then goals either side of the interval from Nabil Baha and Duda Valente firmly placed Malaga in the driving seat.
They finished off the scoring just after the hour mark with Eliseu's second.
Racing Santander left it late, scoring in the second minute of injury time away to Osasuna to claim an important 1-0 victory after a poor start to the season.
Osasuna's Jaroslav Plasil will consider himself unlucky to have been dismissed in the first half for handball inside the area but Ezequiel Garay failed from the penalty spot.
Racing's Juan Varela grabbed the winner, controlling the ball well before firing past the keeper.
Almeria came from two goals down to claim a point in a 2-2 draw away to Getafe.
Ikechukwu Uche and Francisco Casquero appeared to have secured the win before Almeria hit back in the final minutes through Alvaro Negredo and Jose Chico.
An early goal from Angel Lafita after 13 minutes was enough for Deportivo la Coruna to beat Numancia and end their run of a month without a win.