Top seed Djokovic, the runner-up in 2007 and 2010, booked his place in a fifth successive semi-final when Serbian Davis Cup-winning teammate Janko Tipsarevic retired with a left thigh injury.
Djokovic, who was 7-6 (7/2), 6-7 (3/7), 6-0, 3-0 ahead at the time, will face Federer for the fourth year running after the Swiss star demolished Frenchman Jo-Wilfried Tsonga 6-4, 6-3, 6-3.
The winner of that tie will play in a Monday final after besieged organisers surrendered their desperate attempts to shoehorn the remainder of the tournament, which had seen Tuesday and Wednesday washed out, into four days.
The women's final will take place on Sunday instead of Saturday with both men's and women's semi-finals on Saturday.
Djokovic claimed his 62nd win of 2011 when Grand Slam quarter-final debutant Tipsarevic's brave bid was undone by a thigh injury in the third set.
Federer gained revenge for his landmark Wimbledon loss to the Tsonga where the Frenchman had become the first man to defeat the 16-time Grand Slam title winner from two sets to love down.
It will be the fourth successive US Open semi-final meeting between Federer and Djokovic and first since the Swiss ended the Serb's 43-match winning run at the French Open in June.
US Tennis Association officials extended the tournament after leading stars such as Rafael Nadal, Andy Murray and Andy Roddick, who were all facing playing on four consecutive days to make a Sunday final, protested over the schedule.
In contrast, title rivals Djokovic and Federer had both completed their last-16 matches on Monday.
Murray, who made the last eight with a 6-2, 6-3, 6-3 win over America's Donald Young, believes the players need more power at the Grand Slams. (AFP)
