Nadal is 14-0 on clay this season, winning titles in Monte Carlo and Rome. He has lost only two sets during that run, and is looking for a record 18th Masters title, including his previous Madrid title in 2005. Nadal and Andre Agassi have won 17 each, with Roger Federer at 16.
Saturday's win will return Nadal to the No. 2 spot in the rankings.
"Whatever happens (in the final) I can say that this season has been very good. I'd say it's been perfect — or nearly perfect," Nadal said.
The second-seeded Nadal made a string of early unforced errors, dropping serve three times in the opening set. He will play either compatriot David Ferrer or top-ranked Roger Federer in the final.
"I made a lot of mistakes in the first set and Almagro was playing really well," said Nadal. "Because he was attacking me a lot I tried to play safer in the first set — that was a mistake." Almagro appeared on course to finally beating Nadal at his sixth attempt as he kept firing forehand winners past him.
"I've played at a really high level all week," said Almagro. "And I had the best clay-court player in the world against the ropes." Nadal, a four-time French Open champion, broke back in the second game. Almagro won the next game to love when Nadal hit a backhand into the net, then served to go 4-1 up.
Nadal gave a trademark shout and pump of the fist as he broke back again, although the unseeded Almagro coolly saved two break points at 5-4 to close out the set.
In the second set, Nadal's groundstrokes started finding their target and he broke twice as Almagro made 15 unforced errors.
Almagro sent a forehand wide in the second game of the decider to hand Nadal the key break before serving out.
Earlier, Venus Williams reached her first Madrid Masters final by beating Shahar Peer of Israel 6-3, 6-0.
Williams has a 12-1 record on clay this year after having beaten Samantha Stosur and Vera Zvonareva this week.
"I've played so many different players with so many different styles — some play more clay-court tennis, others just hit the ball really hard," Williams said. "So just to come out on top so far is good, and I'm happy with my form and I'm going to try to keep that form tomorrow." The fourth-seeded American will play Aravane Rezai of France after Lucie Safarova of the Czech Republic retired from the second women's semifinal.
Williams looked in control as she secured an early break to go up 3-1. The unseeded Peer responded immediately, earning three break points after firing a forehand pass down the line. Williams saved the first two before hitting a backhand into the net.
Williams eventually found some rhythm on serve, and closed out the first set having broken the Israeli again.
The American started to show her shot range as she led 3-0 in the second set with a deft drop-volley.
Rezai has reached the final in only her second appearance at Madrid.
She converted both of her break points against Safarova to take the first set 6-1 in 23 minutes, firing 15 winners in the process.
Safarova withdrew because of a thigh injury at the start of the second set.
