Djokovic had earlier seen off Stanislas Wawrinka 6-1, 6-4.
The Swiss fifth seed 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, when he won 15 out of 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 stranded 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.
Del Potro held firm till he was broken to love in the fifth game of the decider, but once again he got off the floor immediately to level at 3-3.
Federer made it three straight breaks of serve in the next game, however, and the 32-year-old powered on to take another step towards what would be a 22nd career Masters title, and only his second in Paris after that of 2011.
Djokovic, the second seed, got off to a perfect start in the first quarter-final 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.
Wawrinka struggled to find his range off both flanks.
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.
Two games later he had another chance to break but once again came up short and he immediately paid the price as Djokovic pounced on the Swiss player's errors to take a 4-3 lead.
The Serb served out for the win, Wawrinka ceding match point with a backhand drive that sailed marginally wide.
The consolation was that the Lausanne native had already clinched his first ever place in next week's ATP World Tour Finals in London.