Spain coach Vicente del Bosque was finally able to field his two first-choice strikers, David Villa and Fernando Torres, after the Liverpool player returned from injury. The pair kept Estonian keeper Pavel Londak kept busy throughout much of the match but it was Real Betis defender Juanito who scored first, connecting with a free kick from Barcelona's Xavi Hernandez in the 34th minute.
Valencia striker Villa scored from the penalty spot to make it 2-0 four minutes later after Estonian defender Alo Barengrubhe fouled Torres. Villa, the top scorer at UEFA EURO 2008, has scored in each of Spain's three FIFA World Cup qualifying matches.
Estonia missed a good chance in the middle of the second half when Konstanin Vassiljev burst through the Spanish defence to force Iker Casillas into a diving save. Carlos Puyol stretched Spain's lead with a header in the 69th minute, after Torres picked up a free-kick from Xavi.
The Euro 2008 champions top Group 5 with maximum points, after beating Bosnia-Herzegovina 1-0 and Armenia 4-0. Estonia, who were thrashed 7-0 by Bosnia-Herzogovina last month, remain firmly rooted to the bottom of the group.