But the Serb, ranked number two in the world, surged from behind to defeat Federer 4-6, 6-3, 6-2 in just over two hours, extending his winning streak to 16 matches before going on to win the final against Spaniard David Ferrer.
The result was bittersweet for Federer who earlier in the tournament qualified for the upcoming World Tour Finals in London, starting this week, for the 12th time.
But the Basel native will have a chance for revenge in London on Tuesday night when he plays Djokovic again.
“I was pretty happy with my level of play,” said Federer, reflecting on the game against his rival.
“I wish I could have kept it up for a bit longer and put him under pressure, but Novak battled well to stay in the match in the second set and the third set,” he said.
“I had my chances in the second and third sets,” Federer said.
“Disappointed right now, but overall it was a good week for me.”
Federer and Djokovic will in fact duel twice over a four-day-period in the London tournament, featuring eight of the world’s top players, including Swiss Stanislas Wawrinka.
“It's unusual, no doubt about it to [play] back-to-back matches against Novak,” Federer said, commenting on the unique situation, according to the ATP website.
“I'm always excited about those challenges,” he said.
“I have had a good couple of weeks now,” Federer is quoted as saying.
“Most important [thing] is to recover as much as I can, so maybe the extra day I will get over Novak now, could be an advantage,” he said.
“But I doubt it — he didn't play Basel (the Swiss Indoors, where Federer lost in the final to Juan Martin del Potro).
“So for me, it's really important to rest right now and make sure I sleep enough and do all those things before our match on Tuesday.”
Djokovic, a six-time grand slam winner, last lost a match in the US Open final against Rafael Nadal, who was defeated by his fellow countryman Ferrer in the other semifinal at Paris.
The 26-year-old Belgrade native had to reach the final to have a chance of taking back top spot from Nadal at the World Tour Finals.
"Every time we play it's a great match, challenging and intense," the 26-year-old Belgrade native said of playing against Federer.