Top-seeded Almagro of Spain, the ATP Tour leader with 261 aces, needed only 58 minutes to beat American wild-card Rhyne Williams 6-2, 6-1.
Isner, second in tour aces with 251, recovered from a slow start to top defending champion Juan Monaco of Spain 1-6, 6-4, 6-4 in the other semifinal to set up the booming showdown Sunday.
"Even though I got creamed in that first set, I felt like I was playing pretty good," Isner said. "I felt it was the best I'd played all week. My serve wasn't working in the first set and he was making a lot of returns. It got away from me."
"After that first set, I thought I served smart," Isner said. "I got myself out of several jams the rest of the match so it was very encouraging."
The 6-foot-9 American finished with nine aces against Monaco and has 57 going into the finals, three short of tournament record set by Pete Sampras in 2002.
Isner used his power to good advantage in the final game of the match with serves clocked at 142, 144 and a fault that hit 147 mph at match point. Monaco returned Isner's second serve but Isner sealed the match with a backhand volley.
Almagro added seven aces to his total against Williams.
"I played better today than I did the first two days," Almagro said. "I feel good today. I think he was a little bit tired. I'm happy with my game. I tried to be focused all the time and I moved really good. That's important for me."
Isner lost to Monaco 6-2, 3-6, 6-3 in last year's clay court and he appeared headed for another loss after Monaco broke his serve three times in the opening set.
Isner rallied from 15-40 in the fifth game to deuce but double faulted and hit a backhand into the net at break point. Isner went down at the first set point in the seventh game.
Isner got more aggressive at the start of the second set. He broke Monaco in the fifth game of the second set and in the first game of the third set to fuel his rally.
"He played better than me at the end," Monaco said. "You can play so good one set but that's not enough. He gets confidence when he starts serving well. He played better than me, that's for sure."
Almagro became the first top-seeded player to reach the clay court final since James Blake in 2008.
Almagro, ranked No. 12 in the world, never allowed his 22-year-old foe to get into the match. He broke Williams in the second game of the match that ended with a crowd-pleasing volley exchange.
The first set ended with three straight breaks. Williams was broken in the sixth game on the third break point when Williams hit a forehand beyond the baseline.
Almagro played a poor seventh game and was broken when his backhand sailed wide. Williams was broken with a love eighth game.
Almagro won the first five games of the second set before Williams held in the sixth game but it was over quickly in the seventh game that included at 129 mph ace by Almagro. The Spaniard won at the first match point with a blazing backhand that was unchallenged by Williams.
"I have to give him a lot of credit because he moved the ball around the court really well," Williams said. "He's tops in the world and one of the best clay-courters in the world right now.
"It was fun to see what it was like facing a top guy like that. It was a great experience for me and I enjoyed it even though the result didn't go my way today."
Jamie Murray of Britain and John Peers of Australia upset top-ranked Bob and Mike Bryan of the United States 1-6 7-6 (3) 12-10 in the doubles final. The Bryan brothers had won 19 straight matches in the event.