Tomas Berdych's defeat hands Andy Murray a great chance to move above him into seventh in the race to qualify for the World Tour Finals in London.
World number 113 Andujar was blown away by compatriot Nadal 6-0, 6-4 on Saturday.
In other first-round matches, there were wins for Nikolay Davydenko, qualifier Pablo Andujar and French pair Benoit Paire and Edouard Roger-Vasselin.
Top-seeded Pablo Andujar of Spain, Andreas Seppi of Italy and David Nalbandian of Argentina won on Friday to reach the Serbia Open semi-finals.
Top-seeded Pablo Andujar of Spain rallied past Filippo Volandri of Italy 4-6, 7-5, 6-2 to reach the quarterfinals of the Serbia Open on Thursday.
David Ferrer took a large stride toward back-to-back Mexican Open titles by winning his quarterfinal on Thursday while his main rival and Spanish compatriot Nicolas Almagro lost.
Frederico Gil of Portugal upset fourth-seeded Pablo Andujar of Spain 6-2, 6-1 in the second round of the Vina del Mar VTR Open on Wednesday.
Former finalist Jo-Wilfried Tsonga beat Frederico Gil of Portugal 6-2, 6-2, 6-2 on Saturday to advance to the fourth round at the Australian Open.
Second-seeded Florian Mayer of Germany beat Spain's Pablo Andujar 6-3, 6-1 in the final of the Nastase Tiriac Trophy on Sunday.
Juan Carlos Ferrero overcame a long rain delay on Sunday to defeat Pablo Andujar 6-4, 6-0 in an all-Spanish final of the Mercedes Cup.
After surviving a tough five-setter in his opening match of the French Open, reigning champion Rafael Nadal registered a straight sets victory over countryman Pablo Andujar in the Second Round.
Second seed Fernando Verdasco put an end to a frustrating series of losses by battling to a 6-1, 7-6 (7/5) second round win over Portugal's Frederico Gil at the ATP-WTA Estoril Open on Thursday.
