The Spaniard finished the 169-km leg between Zalla and Vitoria ahead of Kelme team-mate Alejandro Valverde and compatriot Pedro Horrillo.

Zarate, who only turned professional this season, pursued a breakaway group led by Germany's Jens Voigt before overhauling the pack 30km from home.

Valverde's second place meant he regained the overall lead.

Italy's Danilo Di Luca and Davide Rebellin remain in hot pursuit on the same time.

Ghent-Wevelgem

Meanwhile in Belgium, Tom Boonen won the Ghent-Wevelgem spring classic.

The young Quick Step rider restored local pride after German Steffen Wesemann won the Tour of Flanders last Sunday.

Boonen, outsprinted Swede Magnus Backstedt, Estonian Jaan Kirsipuu and a former winner of this race, the American George Hincapie.

British national champion Roger Hammond finished sixth.

The next of the Spring classics is Paris-Roubaix on Eester Sunday.

Ghent-Wevelgem result

1 Tom Boonen (Bel) Quick-Step 4hrs 58mins 47secs
2 Magnus Backstedt (Swe) Alessio-Bianchi at 0.0
3 Jaan Kirsipuu (Est) AG2R-Prevoyance at 0.0
4 George Hincapie (USA) US Postal at 0.0
5 Jimmy Casper (Fra) Cofidis at 0.0
6 Roger Hammond (Gbr) MrBookmaker-Palmans at 0.0
7 Juan Antonio Flecha Giannoni (Spa) Fassa Bortolo at 0.0
8 Vladimir Goussev (Rus) Team CSC at 0.0
9 Sebastien Rosseler (Bel) Relax-Bodysol at 0.0
10 Andreas Klier (Ger) T-Mobile Team at 0.0

Basque stage 3, Zalla-Vitoria

1 Carlos Zarate (Spa) Comunitat Valenciana-Kelme 169km in 4.30.52 (37.44kph)
2 Alejandro Valverde (Spa) Comunitat Valenciana-Kelme 0.21
3 Pedro Horrillo (Spa) Quick Step
4 Matthias Kessler (Ger) T-Mobile
5 Beat Zberg (Swi) Gerolsteiner
6 Jorge Ferrio (Spa) Costa de Almeria
7 Ricardo Serrano (Spa) Caf�s Baqu�
8 Angel Vicioso (Spa) Liberty Seguros
9 Tyler Hamilton (USA) Phonak
10 Francisco Ventoso (Spa) Saunier Duval

Overall standings

1 Alejandro Valverde (Spa) Comunitat Valenciana-Kelme 12.43.50
2 Danilo Di Luca (Ita) Saeco
3 Davide Rebellin (Ita) Gerolsteiner
4 Jorge Ferrio (Spa) Costa de Almeria
5 Samuel Sanchez (Spa) Euskaltel
6 Aitor Osa (Spa) Illes Balears
7 Angel Vicioso (Spa) Liberty Seguros
8 David Etxebarria (Spa) Euskaltel
9 Denis Menchov (Rus) Illes Balears
10 Marco Serrano (Spa) Liberty Seguros