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."
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.