Spain were trailing to a 29th-minute wonder-goal from Jaroslav Plasil, but Villa fired home from the edge of the area in the 69th minute, moving clear of Raul's record of 44 goals and relieving the tension in Granada. Less than five minutes later, he added the second from the penalty spot after Jan Rezek fouled Andres Iniesta in the area. The win sends Spain six points clear of the Czech Republic at the top of Group I with a 100 per cent record.
It looked at the start of the match like being a routine night for the world and European champions as they dominated the early going. Iniesta tested Petr Cech after only two minutes, with the Chelsea goalkeeper fumbling his save before gathering, and moments later Joan Capdevila headed narrowly wide.
Iniesta tried again in the 11th minute, but Cech pushed his shot away. Xavi curled a free-kick wide as Spain continued to probe, while Villa then forced a fantastic save from Cech with a volleyed shot. So it was against the run of play that Plasil fired the visitors ahead with a powerful shot from long range that stunned Iker Casillas and the watching fans.
Following all their early chances, Spain struggled for a response, and it was not until late in the first half that they created any more chances. Gerard Pique headed just wide from Xavi's 42nd minute corner, and Villa then brought another save out of Cech with a header. The goalkeeper then had to punch Xabi Alonso's free-kick clear before holding a Villa shot just before half-time.
Spain were slow to get going in the second half, with a long-range volley from Santi Cazorla which was eye-catching but easy enough for Cech. Sergio Ramos headed wide on the hour mark as the frustrations of the hosts grew.
Villa and Iniesta fired wide, and Cech then tipped a Pique header over the bar, leaving Spain wondering what more they could do to score. The answer came in the 69th minute when Iniesta teed up Villa to fire home left-footed from the edge of the area for his landmark 45th international goal. The 29-year-old added a second moments later after Iniesta was felled, firing his penalty into the bottom left-hand corner.
Fernando Torres had come off the bench, but the goal drought which has afflicted him at Chelsea transferred to the international stage as he missed a good chance from close range in the 76th minute.
Plasil could not repeat his heroics as he sent an 81st-minute free-kick into the wall in a rare chance for the hosts, while the game ended with one final chance for Villa, which Cech parried.