Federer used his strong serve and did not face a break point in cruising past Berdych 6-4, 6-3.
Tsonga edged the unseeded Isner 3-6, 7-6 (1), 7-6 (3) in a gritty contest lasting nearly three hours, a contrast to Federer's 80-minute victory.
The 16-time Grand Slam champion broke the fifth-seeded Berdych's serve at the start of each set to take control.
"I really played great today. I didn't give Tomas much. I was able to play aggressive and serve good, so overall it was a wonderful performance," Federer said. "I just felt like I was reading his serve, I was playing well from the baseline."
Tsonga and Federer will meet for the sixth time this year, and first since the U.S. Open quarterfinals when Federer prevailed. Federer leads 5-3 overall, but two of Tsonga's wins this year came at Wimbledon and the Rogers Cup.
"I have no particular problem playing against him. I'm not afraid of him," Federer said. "I would be afraid of him in the first round, but (not) in the final, when I feel good."
Tsonga won his only Masters title in Paris three years ago, and aims for his eighth career title. He almost threw away the semifinal against Isner. Serving at 40-15 up in the 12th game of the third set, he let Isner back in.
Tsonga saved three match points, with Isner helping him with unforced errors from the baseline.
"You come so close to winning, it gets taken away from you. It wasn't to be," Isner said. "He came up with the goods, hats off to him. That's why he's one of the best players in the world, he came up big."
Isner held serve for the entire match, but Tsonga dominated the tiebreakers to give the final a Frenchman for the fourth successive year.
Tsonga won the first tiebreaker 7-1, and the second 7-3, clinching victory on his first match point with a quick forehand pass that flew past Isner, who was hoping to become the first American to win here since Andre Agassi in 1999.
Berdych, the 2005 champion, looked nervous and failed to find any rhythm as Federer dictated rallies with his unwavering forehand.
Berdych was so impressed that he felt like he was playing against "the old Roger," who won 42 titles, including 11 Grand Slams, between 2004-07.
"We can count the unforced errors he made on the fingers of one hand," Berdych said. "He played like I remember him (playing) a few years ago. Today was pretty much no chance at all for me."
Federer agreed that he was close to his best.
"I take it as a compliment because the Roger Federer of old, he lost five matches a year and won 90 or 80," Federer said. "I think he did really well to hang in there, because I did have more chances than him."
Federer clinched victory on his first match point, on Berdych's serve, when he hit a forehand into the corner that Berdych returned into the net.
The Swiss star, who won his home tournament in Basel last week, will try for his 69th title in his 99th final. He has now reached at least the final of all nine Masters events.
Federer improved to 10-4 against Berdych, who had won their last meeting in straight sets at the Cincinnati quarterfinals in August by attacking Federer's second serve. He got few chances this time, as Federer made 70 percent of first serves.
He won 94 percent of those first serve points in the first set, and 91 percent overall in the match.
"I mixed it up a lot, and I always chose the right moment to do something," said Federer, who is looking to win the Paris title for the first time. "That's a major difference in tennis. I think I did it perfectly today."
When Berdych missed an easy smash at the net in the fourth game, Federer took the reprieve and hit a crisp passing shot into Berdych's feet for a 3-1 lead.
Federer held his serve in a flurry of shots to lead 5-3 in the second set. Another superb winner -- a crosscourt forehand hit with the casual brilliance that is Federer's trademark when on form -- was his 34th of the match. It set up three match points with Berdych 0-40 down.