Djokovic swept into the semi-finals with a rapid-fire 6-1, 6-4 win over Stanislas Wawrinka, while Federer came through a second set wobble to edge Juan Martin del Potro 6-3, 4-6, 6-3.
It will be the 30th meeting between the two, but the first since Djokovic defeated the Swiss great in the ATP World Tour final in London a year ago.
World number one and top seed Rafael Nadal, meanwhile, stayed on course for a record sixth Masters Series title in the same year as he swatted aside the uncertain challenge of French number one Richard Gasquet 6-4, 6-1.
His semi-final opponent will be titleholder and fellow Spaniard David Ferrer who came from a set down to oust Tomas Berdych 4-6, 7-5, 6-3.
Djokovic, Paris Masters champion in 2009, said that Federer was having a strong finish to what had been a disappointing season.
“Roger is probably experiencing the worst season that he had in 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, and we all know how successful a career he has,” the Serb said.
“You cannot underestimate him, although maybe he’s not at the form where he was when he was No. 1 of the world. But I have been watching his matches in Basel last week and here. I think he’s playing really well.”
Fifth seed Federer had lost for the third straight time to the towering Argentine in the final of the Basel tournament on Sunday, on what was home turf for him.
But with Del Potro looking decidedly leg weary from his marathon efforts in recent weeks that have seen him win 15 out of his last 16 matches, Federer was in commanding form from the start.
He broke serve to lead 3-1 and had little difficulty pocketing the first set from there in just 30 minutes, leaving his opponent welded on the baseline with a succession of deft drop shots.
Del Potro tried hard to make a fist of it at the start of the second set, at one point leaping over the net onto his opponent’s side after failing to chase down another Federer drop shot.
The end looked in sight for the South American, but he fought off a series of break points and then summoned up a huge effort in the 10th game to finally take Federer’s serve, levelling the set scores in the process.
But it was all to no avail as Federer got the best of three consecutive breaks of serve in the middle of the decider to take another step towards what would be a 22nd career Masters title, and only his second in Paris after that of 2011.
The win was just the second this year for Federer against a player ranked in the world top 10 and boosted his hopes of salvaging something from what has been a dismal 12 months.
“I knew it was a long time that I had been able to do that (beat a top five player). Every time I played a top 10 I lost, but it was tight.
“So I’m happy now I won against a top 10 again, especially just before London where I will have to play against three top 10 players in a row.”
Second seed Djokovic got off to the perfect start against Wawrinka with a break in the second game to lead 3-0 and he wrapped up the first set at 6-1 after just 26 minutes.
The Swiss seventh seed did have his chances early in the second set, but failed to put away any of the four break points he had in the second game and Djokovic promptly closed the door on him.
For Wawrinka, the consolation was that he had already clinched a place in next week’s ATP World Tour Finals in London, his first appearance in the season-ending finale.
The Paris quarter-finals had flung up a star-studded line-up featuring the eight men who will contest the ATP Tour title in London.
It was the first time since Montreal in 2009 that eight of the top 10 players in the world had reached the quarter-finals of one of the Masters Series tournaments.