Switzerland's former world number one, now ranked sixth, will face second seed Novak Djokovic in the last four in the build-up to next week's ATP World Tour finals in London.
"I knew it was a long time since I had been able to do that," Federer told a news conference after his 6-3 4-6 6-3 victory over the fifth-ranked Argentine.
"So I'm happy now I won against a top 10 (player) again, especially just before London where I will have to play against three top 10 players in a row.
"It seems to be interesting and I'm happy that I made that first step today," he added ahead of next week's ATP World Tour Finals in London.
The 17-times grand slam champion has had his worst season in 10 years, having failed to reach any of the grand slam finals and appearing in only one Masters Series final so far.
His last victory over a top 10 player was in the Australian Open quarter-finals against then eighth-ranked Jo-Wilfried Tsonga of France.
Federer's only title this season came on grass at Halle.
Del Potro beat him in the Basel Open final on Sunday before becoming the highest-ranked player to suffer defeat at the hands of the Swiss in nine months.
"Probably has to be," Federer said when asked if Friday's win had been his best of the season.
"I have had some decent matches along the way ‑ maybe against less famous players than Juan Martin ‑ so I'm happy it worked out well today," added the Swiss, who revived some of his old brilliance at the Paris indoor event.
"I think it was a good match from start to finish. That's definitely good for my confidence, because those are the kind of wins I need right now."
Federer will play at the ATP season finale for the 12th time next week.
(Reporting by Gregory Blachier; Editing by Ken Ferris)
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