Nadal had little trouble extending his winning streak in clay-court semifinals to 46 matches, polishing off his overmatched Spanish countryman after winning the first six games on the outdoor red clay.
Nadal will now have a shot at his fifth title since coming back from a 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."
He will play Stanislas Wawrinka after the 15th-ranked Swiss recovered late on to edge out Tomas Berdych, 6-3, 4-6, 6-4.
Serena Williams and Maria Sharapova will play for both the No. 1 ranking and the women's title after each won her semifinal in straight sets.
Nadal outclassed Andujar at the start.
The clay-court expert's surgical groundstrokes were usually 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 dig out of the hole and 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."
The top-ranked Williams will have a chance to win her 50th career title after beating Sara Errani of Italy 7-5, 6-2, while No. 2 Sharapova recorded her 500th career win at all levels after seeing off Ana Ivanovic 6-4, 6-3.
Both Williams, the defending champion, and Sharapova arrive to their final in good form and with numbers to back up their bid for a title.
Sharapova has won all 10 sets she has played at the tournament, while Williams boasts a 12-2 record against the Russian.
"Of course it's always tough against her," Sharapova said about Williams. "I haven't had a win against her in a long time. But the great thing is that I'm setting myself up in a position where I can try to change that around."
After a skittish start, Williams rolled by 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."
Williams said Sharapova would pose a different challenge from her previous opponents this week.
"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."
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.
Sharapova said she was proud to have notched her 500th win.
"That number is pretty significant," she said. "(And) no, (it) doesn't make me feel like a veteran."
Berdych was on the brink of making his second straight final in Madrid after coming from behind to level with Wawrinka at a set apiece and then building a 4-2 lead in the third.
But the Czech player squandered two break points at that stage and Wawrinka found a second wind to rally back. Wawrinka won the Portugal Open last Sunday.