Top-seeded Djokovic will face Japan's Kei Nishikori and Federer, the number two seed, will play Marin Cilic of Croatia in Saturday's semi-finals.
In 2007, Federer beat Djokovic to win the fourth of his five U.S. Open titles but at Wimbledon two months ago, the Serb triumphed to win his seventh grand slam crown.
The top two seeds will be huge favourites to meet again in Monday's final.
Having under-performed in the two warm-up events in Toronto and Cincinnati, Djokovic has found top form at the right time and saw off Andy Murray in a high-quality quarter-final.
"I was aiming to play my best tennis in the U.S. Open and I believed it was going to happen," said Djokovic, who is chasing a second title in New York.
"Winning against Andy in a grand slam is definitely a confidence boost, and hopefully I can use it for the next match."
Tenth seed Nishikori has shown enormous stamina and resilience to win five-set matches lasting over four hours in each of the past two rounds.
Having had two days off, Nishikori is confident he will be physically up for the battle as he tries to become the first Japanese man to reach a grand slam final.
"I always love to play five sets and I think I have a good record. I get more concentrated and my tennis is getting better playing in the fourth or fifth sets. So these two matches are going to help for sure."

Djokovic said he was expecting nothing other than a tough battle.
"He's a very, very good player (but) I think he's playing best tennis of his life in the last 12 months," he said.
"He serves very efficiently and he's very, very fast, maybe one of the fastest on the Tour and back-to-back five sets is a great sign physically for him."
Federer lost to Djokovic in successive semi-finals at the U.S. Open in 2010 and 2011, saving two match points on both occasions.
The 32-year-old Federer saved two match points himself in beating Gael Monfils of France to make the last four.
The Swiss has been working on his net game under the tutelage of Stefan Edberg and said he would be looking to come forward against Cilic, who ousted Czech Tomas Berdych in the previous round.
"I'm happy I'm spending some time at the net because that's going to keep giving me confidence to keep on doing that as we move along in the tournament," he said.
Cilic is into his second grand slam semi-final, four years after his first and 11 months after returning to the Tour following a four-month ban for failing a drugs test for a tainted supplement.
"Even though I had great success beginning of the year, I felt that I started to play really well somewhere from French Open," he said.
"Since then I think the things are in good place for me and moving really, really good with everything," he said.

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