Vicente Del Bosque's men dominated proceedings this evening despite the manager resting some key players against their closest challengers in Group I
The world champions took the lead early on through Mata after Xavi dissected the home side's defence with a delightful through ball. The Chelsea winger still had a lot to do and he took his finish well, calmly slotting past his club team-mate Petr Cech.
Xabi Alonso added a second midway through the first half after another wonderful assist, this time from David Silva. The Manchester City man picked up possession and drove into the area, before finding Alonso at the back post with an exquisite pass with the outside of his left foot. With the keeper wrong-footed, Alonso had the simplest of tasks, placing the ball into the back of the net from 10 yards out.
Spain looked extremely comfortable as the game approached half-time and Xavi came close to making it three with a wicked free-kick that dipped just over the bar.
The closest Czech Republic came to scoring in the opening 45 minutes was a tame Tomas Rosicky effort that drifted miserably past Iker Casillas' right-hand post.
Fernando Torres had little impact on the game and was replaced by David Villa on the hour mark.
Minutes after Spain made their attacking substitution the Czech Republic followed suit, replacing Milan Baros with the young Tomas Pekhart. The former Tottenham player, an imposing figure at 6 ft 4in, was promoted to the senior team after impressing during the U-21 European Championships this summer.
Soon after, Czech Republic midfielder Tomas Hubschman received a straight red card after 69 minutes for a horrible challenge on Xabi Alonso that led to the Real Madrid midfielder being replaced by Javi Martinez.
The game petered out somewhat following Hubschman's dismissal, with the Czechs struggling to cope with Spain's numerical advantage.
The visitors came close to scoring a third on a number of occasions. Martinez was unfortunate to see his effort trickle past the post after bursting through the heart of the Czech Republic defence and again came close just minutes later, only to see his deflected effort cannon back off the crossbar with Cech well-beaten.
Spain had already secured a place in the finals next summer before the game this evening but the Czechs' own qualification remains in the balance following this defeat. With Del Bosque resting a number of players Michal Bilek will be disappointed at the manner of his team's defeat this evening, with his team looking second best throughout the game.