Federer, Djokovic in semis
The Swiss, who had lost his prior three encounters with the towering Del Potro including the Basel Open final on Sunday, will play a Masters Series semifinal for only the second time this year.
He will face Djokovic, who hammered Swiss Stanislas Wawrinka 6-1 6-4, for the first time since last year's ATP World Tour finals.
Federer has a 16-13 record against the Serb, who won their last meeting in London a year ago.
"Roger is probably experiencing the worst season that he's had in the last 10 years, but he's still a player to beat in every tournament, because he's Roger Federer, because he has won 17 Grand Slams," Djokovic told a news conference.
"You can't underestimate him, although maybe he's not at the form where he was when he was number one in the world. But I have been watching his matches in Basel last week and here. I think he's playing really well."
Fifth seeded Federer proved Djokovic right in the first set of his quarterfinal against Del Potro, reviving his old brilliance to hit 17 winners.
However, he lost a bit a sharpness in the second set and the Argentine made the most of it.
Del Potro, who did not have a single break chance until the second set's 10th game, converted his second to force Federer into a decisive set.
Cheered on by the packed crowd, 2011 Paris Masters winner Federer played more aggressively and broke Del Potro's serve in the seventh game.
Djokovic, the 2009 Paris Masters champion, had to battle through five sets to prevail in his last two matches against Wawrinka but started fast this time out to take a 3-0 lead.
He never loosened his grip and left the seventh seeded Swiss with the feeling he had no chance of victory.
"When he plays that good it's very difficult, especially on this surface where he's the best, I believe," Wawrinka said.
World number one Rafael Nadal faces local favourite Richard Gasquet in the late session's first match before title holder David Ferrer takes on sixth-seed Czech Tomas Berdych.
Earlier on Thursday, World No 1 Rafael Nadal broke the stubborn resistance of Poland’s Jerzy Janowicz’s to win 7-5, 6-4 and reach the last eight of the Paris Masters on Thursday.
In the semifinals of the Paris event -- one of only three Masters titles the Spaniard has yet to win -- Nadal faces local favourite Richard Gasquet who, along with Swiss Stanislas Wawrinka, have completed the ATP World Tour finals line-up.
Both players won their third-round matches at Bercy but it was Canadian Milos Raonic’s defeat by Tomas Berdych that sent them into next week’s season-ending showdown in London.
They join Nadal, Novak Djokovic, David Ferrer, Juan Martin del Potro, Berdych and Roger Federer in next week’s showpiece. All eight reached the Paris Masters quarterfinals on Friday.