Nadal had little trouble extending his winning streak in clay-court semifinals to 46 matches, quickly finishing his overmatched countryman after winning the first six games.
Nadal can win his fifth title since coming back from seven-month layoff healing his left knee.
"I couldn't have asked for a better run of results," said Nadal, a two-time champion in the Spanish capital. "Five months ago I wouldn't have dreamed of this return. I want to thank all those who supported me through that time."
The Spaniard will play Stanislas Wawrinka after the 15th-ranked Swiss recovered late to defeat Tomas Berdych 6-3, 4-6, 6-4.
Serena Williams and Maria Sharapova will meet for the No. 1 ranking and the women's title after winning semifinals in straight sets.
Nadal dominated the outclassed Andujar.
The clay-court expert's groundstrokes usually were enough to force Andujar to make errors - and if not, Nadal knew when to go for a winner or approach the net to finish off the point.
The worst moment for the 113th-ranked Andujar came when he ceded his third straight service game with a double fault.
But in the second set Andujar shook off his jitters and had three break points for a 4-2 lead, only for Nadal to hold his serve.
"I played a very, very good first set, playing aggressively," Nadal said. "Pablo played more aggressively in the second set and had a chance at a break, but luckily it got away from him."
Andujar continued to prove feisty, but Nadal hit a winner to set up a break point for 5-4 that he converted when Andujar's drop shot fell short.
The top-ranked Williams will have a chance to win her 50th title after beating Sara Errani of Italy 7-5, 6-2. No. 2 Sharapova got her 500th win at all levels after defeating Ana Ivanovic 6-4, 6-3.
Sharapova has won all 10 sets she has played on Madrid's outdoor red clay court. Williams, however, boasts a 12-2 record against the Russian.
After a skittish start, Williams dominated Errani and broke her final service game in both sets.
"I feel I played solid," Williams said. "In the second set more than in the first, I made a few less errors, which is something I needed to do."
The defending champion improved to 5-0 against the seventh-ranked Errani and to 30-2 this year.
Williams said Sharapova will pose a difficult challenge.
"I feel this whole tournament I have only played clay-court opponents," said Williams. "All have been smaller than me. Tomorrow will be a different game, more power."
Williams struggled with her shot-making early, uncharacteristically misfiring on three smashes in the first set, which she still managed to pull out after falling behind 3-1.
The 15-time Grand Slam winner then started clicking with her serve and held two games to love, but she needed four set points before finally breaking Errani with a forehand winner placed just inside the line to grab the lead.
Ahead a set, Williams pressed her advantage and eased through the second.
On Sunday, Williams will play her first final on red clay since 2002. Last year's trophy at the Caja Magica came on the experimental blue clay surface that was removed following players' complaints it was too slippery.
After Sharapova won the first set, Ivanovic opened a 2-0 lead in the second. But Sharapova responded and stole her serve twice, sealing the second break with a lob over the top of her Serb rival.
Sharapova has beaten Ivanovic, a fellow former No. 1, in their last six meetings.
Berdych was on the brink of making his second straight final in Madrid after coming from behind to tie Wawrinka at a set apiece and then building a 4-2 lead in the third. But the Czech squandered two break points at that stage and Wawrinka found a second wind to rally back. Wawrinka won the Portugal Open last Sunday.