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 Sunday's showpiece.