The 11-time grand slam winner posted a 6-0 6-4 result to reach his seventh final in as many tournaments this year.
Nadal ran away with the opening set against Andujar, winning 88 per cent of his first serves in a one-sided contest.
Andujar settled better in the second set, improving his service game and carving out three break point opportunities but without being able to capitalise.
That proved costly and Nadal gained the crucial break in game eight when Andujar hit a weak forehand into the net.
That left the fifth seed serving for the match and he wrapped things up after one hour and 17 minutes with an unreturnable crosscourt forehand.
Nadal is bidding to win his third Madrid title and will face either Stanislas Wawrinka or Tomas Berdych in tomorrow's showpiece.
In the women's tournament, the top two seeds will meet in what is set to be an intriguing final after Serena Williams and Maria Sharapova came through their respective semis in straight sets.
Williams, the world number one, beat Sara Errani 7-5 6-2 and will be aiming to lift her 50th WTA title tomorrow.
The American twice fought back from a break down to win a closely contested opening set before dominating the second to see off the seventh-seeded Italian.
It will be Williams first final on clay since 2002 and overall she was satisfied with today's performance.
''I guess I'm a little happy,'' she told www.stator.com.
''I feel that I played solid. In the second set more than the first I made less errors, which was something that I really needed to do today.''
Second seed Sharapova was a 6-4 6-3 winner over Serbia's Ana Ivanovic, edging a tight first set and then coming back from a break down in the second.
The Russian has a poor record against Williams, winning just two of their 14 encounters and with her last victory over the American back in 2004.
However, Sharapova is up for the challenge and said: ''It's always tough against her.
''I haven't had a win against her in a long time, but the great thing is I'm setting myself up in a position where I can try to change that around.''