Cancelo put the 2019 champions in front in the 33rd minute of the League A Group 2 contest, blasting the ball past Czech goalkeeper Jindrich Stanek from a tight angle after good work on the right before Guedes struck.
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Valencia's forward found himself in space and tucked in from a similar position to Cancelo to double Portugal's lead as Fernando Santos`s side tightened their grip on the top spot in the group with seven points from three matches. Portugal travels to Switzerland on Sunday, having sealed an emphatic 4-0 home victory in their previous meeting.
Whereas in the other game between Spain and Switzerland, An early goal from Pablo Sarabia earned Spain a 1-0 win in Switzerland on Thursday, their first victory of this year's UEFA Nations League.
Last year's finalists dominated the game from the start but were only able to score once when Sarabia struck from close range in the 12th minute following a low cross by Marcos Llorente.
The Atletico Madrid winger found Sarabia ghosting in between two opponents inside the six-yard box and he scored with a first-time shot. Spain has five points from their opening three Group A2 matches to sit two behind leaders Portugal and two ahead of third-placed Czech Republic.
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Switzerland have suffered three consecutive losses and are winless in their last five games since qualifying for this year's World Cup. Spain hosts the Czechs in Malaga and Switzerland entertains Portugal in Geneva on Sunday.
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(With inputs from Reuters)